Hmdb loader

Showing metabocard for Graecunin D (HMDB0039422)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:53:06 UTC
Update Date2022-03-07 02:56:12 UTC
HMDB IDHMDB0039422
Secondary Accession Numbers
  • HMDB39422
Metabolite Identification
Common NameGraecunin D
DescriptionGraecunin D belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. Graecunin D has been detected, but not quantified in, fenugreeks (Trigonella foenum-graecum) and herbs and spices. This could make graecunin D a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Graecunin D.
Structure
Data?1563863372
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039422 (Graecunin D)


  Mrv0541 02241221012D          

 77 80  0  0  1  0            999 V2000
    8.8423    1.3716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5567    0.9591    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5567    0.1341    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.8423   -0.2784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3272   -0.9459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1278    0.1341    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.4133   -0.2784    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.4133   -1.1034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1278   -1.5159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8815   -1.1804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4335   -1.7935    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.0210   -2.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2760   -3.2926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7239   -3.9056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9169   -3.7341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6620   -2.9495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2140   -2.3364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6989    0.1341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6989    0.9591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9844   -0.2784    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2699    0.1341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5555   -0.2784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8410    0.1341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5555   -1.1034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2712   -0.2784    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9857    0.1341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9857    0.9591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7002   -0.2784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4146    0.1341    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.1291   -0.2784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1291   -1.1034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8436    0.1341    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.8436    0.9591    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.5580    1.3716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1291    1.3716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5580   -0.2784    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   18.8449   -0.2784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9870   -1.1034    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   17.4159   -1.1034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   18.3250   -1.7639    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   19.7228   -2.0610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5074   -1.8061    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   17.8105   -4.1849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9900   -4.0986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   19.6497   -5.8409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3905   -4.5241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8543   -5.2468    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.6828   -6.0537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2959   -6.6058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8982   -6.3087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.2712    1.3716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  7  6  1  1  0  0  0
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  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
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 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
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 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
  9 17  1  0  0  0  0
  7 18  1  0  0  0  0
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 18 20  1  0  0  0  0
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 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
  3 25  1  6  0  0  0
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 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
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 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  6  0  0  0
 32 36  1  6  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
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 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
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 49 50  1  0  0  0  0
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 48 52  1  0  0  0  0
 52 53  1  0  0  0  0
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 61 62  2  0  0  0  0
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 73 75  1  0  0  0  0
 75 76  1  0  0  0  0
  2 77  1  1  0  0  0
M  CHG  1  76   1
M  END
Download

3D MOL for HMDB0039422 (Graecunin D)

HMDB0039422
     RDKit          3D
Graecunin D
141144  0  0  0  0  0  0  0  0999 V2000
    4.8937    1.6204    2.2431 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2884    1.1612    1.8286 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.7737    0.2370    2.8011 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2123    0.5402    0.4860 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3093   -0.6028    0.5078 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9532   -1.2934   -0.6567 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4601   -0.9366   -1.7533 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0197   -2.4126   -0.6878 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3214   -2.6913    0.5658 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4320   -1.7313    1.1050 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3412   -0.6577    0.3841 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6232   -1.8048    2.3307 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2165   -1.5050    2.1021 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4703   -1.0348    1.0051 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0331   -0.7705   -0.0870 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9658   -0.8095    1.0512 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5607   -1.3710    2.3307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0644   -1.1216    2.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6090   -1.7023    3.6081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8947   -2.2946    4.4297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9592   -1.5815    3.8741 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5959   -1.3689   -0.0821 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6211   -0.9062   -0.9543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    0.2085   -0.7298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0000   -1.7743   -2.0198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7629   -1.2637   -3.4481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4249   -2.4151   -4.2610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0646   -3.3139   -3.1835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3921   -2.2228   -2.2238 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5771   -1.7791   -1.6680 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.9546   -2.2074   -1.6969 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -8.9819   -1.2934   -1.4891 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0076   -0.4049   -1.3044 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1053   -0.2881   -1.9662 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9922    0.6446   -0.1978 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.1452    0.1528    0.7350 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2902    1.0802    1.8992 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6253    0.8456    3.0745 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7687    1.7319    4.1118 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5510    2.8635    4.0577 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6930    3.7539    5.1235 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2321    3.1062    2.8582 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0794    2.2020    1.8147 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5226    1.8692   -0.7522 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9274    3.1358   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8507    3.2044    0.1192 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4674    4.4038   -1.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6770    4.1262   -1.8563 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.7775   -3.0709    3.0728 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1695   -3.4413    3.4937 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0088   -2.9541    4.2785 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5425    0.1907   -0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7251   -1.0511   -0.4118 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5437    1.0829   -0.3717 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8302    0.9061   -0.9564 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0098    2.0479   -1.9196 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2377    2.1927   -2.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5067    1.7137   -3.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7556    2.0612   -4.2896 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.3479    2.7470   -3.3076 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5925    3.3203   -3.2093 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9150    3.9957   -2.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9914    4.1025   -1.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7723    3.5232   -1.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4204    2.8377   -2.2814 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9741    0.7499   -0.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8570    0.9585    1.1843 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2067    0.3525   -0.6281 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.3967    0.1405    0.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2563   -1.0017    1.0613 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1914   -1.6168    1.1813 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  1  53   1
M  END
Download

3D SDF for HMDB0039422 (Graecunin D)


  Mrv0541 02241221012D          

 77 80  0  0  1  0            999 V2000
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 60 61  1  0  0  0  0
 61 62  2  0  0  0  0
 61 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  2  0  0  0  0
 66 67  1  0  0  0  0
 67 68  2  0  0  0  0
 68 69  1  0  0  0  0
 69 70  2  0  0  0  0
 65 70  1  0  0  0  0
 68 71  1  0  0  0  0
 63 72  1  6  0  0  0
 72 73  1  0  0  0  0
 73 74  2  0  0  0  0
 73 75  1  0  0  0  0
 75 76  1  0  0  0  0
  2 77  1  1  0  0  0
M  CHG  1  76   1
M  END
> <DATABASE_ID>
HMDB0039422

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H](O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](CCC(O)=O)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(O)=O)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)C[NH3+])[C@@H](C)O)C(=O)N[C@@H](CC1=CNC2=CC=CC=C12)C(=O)NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C48H63N11O18/c1-23(60)40(46(75)51-21-36(64)57-41(24(2)61)47(76)55-32(42(71)52-22-39(69)70)17-26-20-50-29-7-4-3-6-28(26)29)58-43(72)30(13-14-37(65)66)54-45(74)34-8-5-15-59(34)48(77)33(18-38(67)68)56-44(73)31(53-35(63)19-49)16-25-9-11-27(62)12-10-25/h3-4,6-7,9-12,20,23-24,30-34,40-41,50,60-62H,5,8,13-19,21-22,49H2,1-2H3,(H,51,75)(H,52,71)(H,53,63)(H,54,74)(H,55,76)(H,56,73)(H,57,64)(H,58,72)(H,65,66)(H,67,68)(H,69,70)/p+1/t23-,24-,30+,31+,32+,33+,34+,40+,41+/m1/s1

> <INCHI_KEY>
YYYJTUAEGPSBSQ-GZCAAYOFSA-O

> <FORMULA>
C48H64N11O18

> <MOLECULAR_WEIGHT>
1083.0847

> <EXACT_MASS>
1082.443079299

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
105.36775608186355

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
16

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-4-{[(2S)-1-[(2S)-2-[(2S)-2-(2-azaniumylacetamido)-3-(4-hydroxyphenyl)propanamido]-3-carboxypropanoyl]pyrrolidin-2-yl]formamido}-4-{[(1S,2R)-1-[({[(1S,2R)-1-{[(1S)-1-[(carboxymethyl)carbamoyl]-2-(1H-indol-3-yl)ethyl]carbamoyl}-2-hydroxypropyl]carbamoyl}methyl)carbamoyl]-2-hydroxypropyl]carbamoyl}butanoic acid

> <ALOGPS_LOGP>
-1.06

> <JCHEM_LOGP>
-8.569980557288035

> <ALOGPS_LOGS>
-4.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.61958551155898

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1090547004553084

> <JCHEM_PKA_STRONGEST_BASIC>
7.829372721014732

> <JCHEM_POLAR_SURFACE_AREA>
469.12999999999994

> <JCHEM_REFRACTIVITY>
272.7303000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
29

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.94e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S)-4-{[(2S)-1-[(2S)-2-[(2S)-2-(2-ammonioacetamido)-3-(4-hydroxyphenyl)propanamido]-3-carboxypropanoyl]pyrrolidin-2-yl]formamido}-4-{[(1S,2R)-1-[({[(1S,2R)-1-{[(1S)-1-(carboxymethylcarbamoyl)-2-(1H-indol-3-yl)ethyl]carbamoyl}-2-hydroxypropyl]carbamoyl}methyl)carbamoyl]-2-hydroxypropyl]carbamoyl}butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039422 (Graecunin D)

HMDB0039422
     RDKit          3D
Graecunin D
141144  0  0  0  0  0  0  0  0999 V2000
    4.8937    1.6204    2.2431 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2884    1.1612    1.8286 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.7737    0.2370    2.8011 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2123    0.5402    0.4860 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3093   -0.6028    0.5078 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9532   -1.2934   -0.6567 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4601   -0.9366   -1.7533 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0197   -2.4126   -0.6878 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3214   -2.6913    0.5658 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4320   -1.7313    1.1050 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3412   -0.6577    0.3841 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6232   -1.8048    2.3307 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2165   -1.5050    2.1021 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4703   -1.0348    1.0051 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0331   -0.7705   -0.0870 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9658   -0.8095    1.0512 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5607   -1.3710    2.3307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0644   -1.1216    2.3576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6090   -1.7023    3.6081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8947   -2.2946    4.4297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9592   -1.5815    3.8741 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5959   -1.3689   -0.0821 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6211   -0.9062   -0.9543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1110    0.2085   -0.7298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0000   -1.7743   -2.0198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7629   -1.2637   -3.4481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4249   -2.4151   -4.2610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0646   -3.3139   -3.1835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3921   -2.2228   -2.2238 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5771   -1.7791   -1.6680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4268   -0.7031   -0.9260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9546   -2.2074   -1.6969 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.2396   -3.2669   -2.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0573   -2.9143   -4.1298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1012   -3.8723   -4.9768 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8377   -1.6650   -4.7042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9819   -1.2934   -1.4891 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0076   -0.4049   -1.3044 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1053   -0.2881   -1.9662 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9922    0.6446   -0.1978 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.1452    0.1528    0.7350 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2902    1.0802    1.8992 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6253    0.8456    3.0745 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7687    1.7319    4.1118 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5510    2.8635    4.0577 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6930    3.7539    5.1235 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2321    3.1062    2.8582 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0794    2.2020    1.8147 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5226    1.8692   -0.7522 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9274    3.1358   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8507    3.2044    0.1192 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4674    4.4038   -1.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6770    4.1262   -1.8563 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.7775   -3.0709    3.0728 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1695   -3.4413    3.4937 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0088   -2.9541    4.2785 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5425    0.1907   -0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7251   -1.0511   -0.4118 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5437    1.0829   -0.3717 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8302    0.9061   -0.9564 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0098    2.0479   -1.9196 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2377    2.1927   -2.6525 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5067    1.7137   -3.9424 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7556    2.0612   -4.2896 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.3479    2.7470   -3.3076 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5925    3.3203   -3.2093 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9150    3.9957   -2.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9914    4.1025   -1.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7723    3.5232   -1.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4204    2.8377   -2.2814 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9741    0.7499   -0.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8570    0.9585    1.1843 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2067    0.3525   -0.6281 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.3967    0.1405    0.1191 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2563   -1.0017    1.0613 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1914   -1.6168    1.1813 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3568   -1.4065    1.8421 O   0  0  0  0  0  0  0  0  0  0  0  0
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 33 34  1  0
 34 35  2  0
 34 36  1  0
 32 37  1  0
 37 38  1  0
 38 39  2  0
 38 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  2  0
 43 44  1  0
 44 45  2  0
 45 46  1  0
 45 47  1  0
 47 48  2  0
 40 49  1  0
 49 50  1  0
 50 51  2  0
 50 52  1  0
 52 53  1  0
 12 54  1  0
 54 55  1  0
 54 56  1  0
  4 57  1  0
 57 58  2  0
 57 59  1  0
 59 60  1  0
 60 61  1  0
 61 62  1  0
 62 63  2  0
 63 64  1  0
 64 65  1  0
 65 66  2  0
 66 67  1  0
 67 68  2  0
 68 69  1  0
 69 70  2  0
 60 71  1  0
 71 72  2  0
 71 73  1  0
 73 74  1  0
 74 75  1  0
 75 76  2  0
 75 77  1  0
 29 25  1  0
 48 42  1  0
 70 62  1  0
 70 65  1  0
  1 78  1  0
  1 79  1  0
  1 80  1  0
  2 81  1  6
  3 82  1  0
  4 83  1  6
  5 84  1  0
  8 85  1  0
  8 86  1  0
  9 87  1  0
 12 88  1  1
 13 89  1  0
 16 90  1  1
 17 91  1  0
 17 92  1  0
 18 93  1  0
 18 94  1  0
 21 95  1  0
 22 96  1  0
 25 97  1  1
 26 98  1  0
 26 99  1  0
 27100  1  0
 27101  1  0
 28102  1  0
 28103  1  0
 32104  1  1
 33105  1  0
 33106  1  0
 36107  1  0
 37108  1  0
 40109  1  1
 41110  1  0
 41111  1  0
 43112  1  0
 44113  1  0
 46114  1  0
 47115  1  0
 48116  1  0
 49117  1  0
 52118  1  0
 52119  1  0
 53120  1  0
 53121  1  0
 53122  1  0
 54123  1  6
 55124  1  0
 55125  1  0
 55126  1  0
 56127  1  0
 59128  1  0
 60129  1  6
 61130  1  0
 61131  1  0
 63132  1  0
 64133  1  0
 66134  1  0
 67135  1  0
 68136  1  0
 69137  1  0
 73138  1  0
 74139  1  0
 74140  1  0
 77141  1  0
M  CHG  1  53   1
M  END
Download

PDB for HMDB0039422 (Graecunin D)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      16.506   2.560   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.839   1.790   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.839   0.250   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.506  -0.520   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      17.411  -1.766   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      15.172   0.250   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      13.838  -0.520   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.838  -2.060   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.172  -2.830   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.579  -2.203   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      17.609  -3.348   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      16.839  -4.681   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.315  -6.146   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      16.285  -7.290   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.778  -6.970   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.302  -5.506   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      15.333  -4.361   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.505   0.250   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      12.505   1.790   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      11.171  -0.520   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       9.837   0.250   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.504  -0.520   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       7.170   0.250   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       8.504  -2.060   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0      19.173  -0.520   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      20.507   0.250   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      20.507   1.790   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      21.840  -0.520   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      23.174   0.250   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      24.508  -0.520   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      24.508  -2.060   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      25.841   0.250   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      25.841   1.790   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      27.175   2.560   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      24.508   2.560   0.000  0.00  0.00           O+0
HETATM   36  N   UNK     0      27.175  -0.520   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0      28.509   0.250   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      28.509   1.790   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      29.842  -0.520   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      31.176   0.250   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      32.510  -0.520   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      33.843   0.250   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      33.843   1.790   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      35.177  -0.520   0.000  0.00  0.00           O+0
HETATM   45  N   UNK     0      29.842  -2.060   0.000  0.00  0.00           N+0
HETATM   46  C   UNK     0      31.176  -2.830   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      32.510  -2.060   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      31.176  -4.370   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      29.930  -5.275   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      30.406  -6.740   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      31.946  -6.740   0.000  0.00  0.00           C+0
HETATM   52  N   UNK     0      32.422  -5.275   0.000  0.00  0.00           N+0
HETATM   53  C   UNK     0      33.887  -4.799   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      34.207  -3.293   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      35.031  -5.829   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      36.496  -5.354   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      36.816  -3.847   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      38.280  -3.371   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      35.671  -2.817   0.000  0.00  0.00           O+0
HETATM   60  N   UNK     0      34.711  -7.336   0.000  0.00  0.00           N+0
HETATM   61  C   UNK     0      33.246  -7.812   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      31.715  -7.651   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      32.926  -9.318   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      34.070 -10.349   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      35.535  -9.873   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      35.855  -8.366   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      37.320  -7.890   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      38.464  -8.921   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      38.144 -10.427   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      36.679 -10.903   0.000  0.00  0.00           C+0
HETATM   71  O   UNK     0      39.929  -8.445   0.000  0.00  0.00           O+0
HETATM   72  N   UNK     0      31.461  -9.794   0.000  0.00  0.00           N+0
HETATM   73  C   UNK     0      31.141 -11.300   0.000  0.00  0.00           C+0
HETATM   74  O   UNK     0      32.286 -12.331   0.000  0.00  0.00           O+0
HETATM   75  C   UNK     0      29.677 -11.776   0.000  0.00  0.00           C+0
HETATM   76  N   UNK     0      29.356 -13.282   0.000  0.00  0.00           N+1
HETATM   77  O   UNK     0      19.173   2.560   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   77                                                  
CONECT    3    2    4   25                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12    9                                                  
CONECT   18    7   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25    3   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   36                                                  
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   32   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   45                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45   39   46                                                       
CONECT   46   45   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   49   52                                                  
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   48   53                                                  
CONECT   53   52   54   55                                                  
CONECT   54   53                                                            
CONECT   55   53   56   60                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57                                                            
CONECT   60   55   61                                                       
CONECT   61   60   62   63                                                  
CONECT   62   61                                                            
CONECT   63   61   64   72                                                  
CONECT   64   63   65                                                       
CONECT   65   64   66   70                                                  
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69   71                                                  
CONECT   69   68   70                                                       
CONECT   70   69   65                                                       
CONECT   71   68                                                            
CONECT   72   63   73                                                       
CONECT   73   72   74   75                                                  
CONECT   74   73                                                            
CONECT   75   73   76                                                       
CONECT   76   75                                                            
CONECT   77    2                                                            
MASTER        0    0    0    0    0    0    0    0   77    0  160    0
END
Download

3D PDB for HMDB0039422 (Graecunin D)

COMPND    HMDB0039422
HETATM    1  C1  UNL     1       4.894   1.620   2.243  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.288   1.161   1.829  1.00  0.00           C  
HETATM    3  O1  UNL     1       6.774   0.237   2.801  1.00  0.00           O  
HETATM    4  C3  UNL     1       6.212   0.540   0.486  1.00  0.00           C  
HETATM    5  N1  UNL     1       5.309  -0.603   0.508  1.00  0.00           N  
HETATM    6  C4  UNL     1       4.953  -1.293  -0.657  1.00  0.00           C  
HETATM    7  O2  UNL     1       5.460  -0.937  -1.753  1.00  0.00           O  
HETATM    8  C5  UNL     1       4.020  -2.413  -0.688  1.00  0.00           C  
HETATM    9  N2  UNL     1       3.321  -2.691   0.566  1.00  0.00           N  
HETATM   10  C6  UNL     1       2.432  -1.731   1.105  1.00  0.00           C  
HETATM   11  O3  UNL     1       2.341  -0.658   0.384  1.00  0.00           O  
HETATM   12  C7  UNL     1       1.623  -1.805   2.331  1.00  0.00           C  
HETATM   13  N3  UNL     1       0.217  -1.505   2.102  1.00  0.00           N  
HETATM   14  C8  UNL     1      -0.470  -1.035   1.005  1.00  0.00           C  
HETATM   15  O4  UNL     1       0.033  -0.770  -0.087  1.00  0.00           O  
HETATM   16  C9  UNL     1      -1.966  -0.809   1.051  1.00  0.00           C  
HETATM   17  C10 UNL     1      -2.561  -1.371   2.331  1.00  0.00           C  
HETATM   18  C11 UNL     1      -4.064  -1.122   2.358  1.00  0.00           C  
HETATM   19  C12 UNL     1      -4.609  -1.702   3.608  1.00  0.00           C  
HETATM   20  O5  UNL     1      -3.895  -2.295   4.430  1.00  0.00           O  
HETATM   21  O6  UNL     1      -5.959  -1.582   3.874  1.00  0.00           O  
HETATM   22  N4  UNL     1      -2.596  -1.369  -0.082  1.00  0.00           N  
HETATM   23  C13 UNL     1      -3.621  -0.906  -0.954  1.00  0.00           C  
HETATM   24  O7  UNL     1      -4.111   0.208  -0.730  1.00  0.00           O  
HETATM   25  C14 UNL     1      -4.000  -1.774  -2.020  1.00  0.00           C  
HETATM   26  C15 UNL     1      -3.763  -1.264  -3.448  1.00  0.00           C  
HETATM   27  C16 UNL     1      -4.425  -2.415  -4.261  1.00  0.00           C  
HETATM   28  C17 UNL     1      -5.065  -3.314  -3.184  1.00  0.00           C  
HETATM   29  N5  UNL     1      -5.392  -2.223  -2.224  1.00  0.00           N  
HETATM   30  C18 UNL     1      -6.577  -1.779  -1.668  1.00  0.00           C  
HETATM   31  O8  UNL     1      -6.427  -0.703  -0.926  1.00  0.00           O  
HETATM   32  C19 UNL     1      -7.955  -2.207  -1.697  1.00  0.00           C  
HETATM   33  C20 UNL     1      -8.240  -3.267  -2.748  1.00  0.00           C  
HETATM   34  C21 UNL     1      -8.057  -2.914  -4.130  1.00  0.00           C  
HETATM   35  O9  UNL     1      -8.101  -3.872  -4.977  1.00  0.00           O  
HETATM   36  O10 UNL     1      -7.838  -1.665  -4.704  1.00  0.00           O  
HETATM   37  N6  UNL     1      -8.982  -1.293  -1.489  1.00  0.00           N  
HETATM   38  C22 UNL     1     -10.008  -0.405  -1.304  1.00  0.00           C  
HETATM   39  O11 UNL     1     -11.105  -0.288  -1.966  1.00  0.00           O  
HETATM   40  C23 UNL     1      -9.992   0.645  -0.198  1.00  0.00           C  
HETATM   41  C24 UNL     1     -11.145   0.153   0.735  1.00  0.00           C  
HETATM   42  C25 UNL     1     -11.290   1.080   1.899  1.00  0.00           C  
HETATM   43  C26 UNL     1     -10.625   0.846   3.075  1.00  0.00           C  
HETATM   44  C27 UNL     1     -10.769   1.732   4.112  1.00  0.00           C  
HETATM   45  C28 UNL     1     -11.551   2.863   4.058  1.00  0.00           C  
HETATM   46  O12 UNL     1     -11.693   3.754   5.124  1.00  0.00           O  
HETATM   47  C29 UNL     1     -12.232   3.106   2.858  1.00  0.00           C  
HETATM   48  C30 UNL     1     -12.079   2.202   1.815  1.00  0.00           C  
HETATM   49  N7  UNL     1     -10.523   1.869  -0.752  1.00  0.00           N  
HETATM   50  C31 UNL     1      -9.927   3.136  -0.570  1.00  0.00           C  
HETATM   51  O13 UNL     1      -8.851   3.204   0.119  1.00  0.00           O  
HETATM   52  C32 UNL     1     -10.467   4.404  -1.132  1.00  0.00           C  
HETATM   53  N8  UNL     1     -11.677   4.126  -1.856  1.00  0.00           N1+
HETATM   54  C33 UNL     1       1.777  -3.071   3.073  1.00  0.00           C  
HETATM   55  C34 UNL     1       3.169  -3.441   3.494  1.00  0.00           C  
HETATM   56  O14 UNL     1       1.009  -2.954   4.278  1.00  0.00           O  
HETATM   57  C35 UNL     1       7.542   0.191  -0.114  1.00  0.00           C  
HETATM   58  O15 UNL     1       7.725  -1.051  -0.412  1.00  0.00           O  
HETATM   59  N9  UNL     1       8.544   1.083  -0.372  1.00  0.00           N  
HETATM   60  C36 UNL     1       9.830   0.906  -0.956  1.00  0.00           C  
HETATM   61  C37 UNL     1      10.010   2.048  -1.920  1.00  0.00           C  
HETATM   62  C38 UNL     1      11.238   2.193  -2.652  1.00  0.00           C  
HETATM   63  C39 UNL     1      11.507   1.714  -3.942  1.00  0.00           C  
HETATM   64  N10 UNL     1      12.756   2.061  -4.290  1.00  0.00           N  
HETATM   65  C40 UNL     1      13.348   2.747  -3.308  1.00  0.00           C  
HETATM   66  C41 UNL     1      14.593   3.320  -3.209  1.00  0.00           C  
HETATM   67  C42 UNL     1      14.915   3.996  -2.067  1.00  0.00           C  
HETATM   68  C43 UNL     1      13.991   4.102  -1.004  1.00  0.00           C  
HETATM   69  C44 UNL     1      12.772   3.523  -1.139  1.00  0.00           C  
HETATM   70  C45 UNL     1      12.420   2.838  -2.281  1.00  0.00           C  
HETATM   71  C46 UNL     1      10.974   0.750  -0.064  1.00  0.00           C  
HETATM   72  O16 UNL     1      10.857   0.958   1.184  1.00  0.00           O  
HETATM   73  N11 UNL     1      12.207   0.352  -0.628  1.00  0.00           N  
HETATM   74  C47 UNL     1      13.397   0.140   0.119  1.00  0.00           C  
HETATM   75  C48 UNL     1      13.256  -1.002   1.061  1.00  0.00           C  
HETATM   76  O17 UNL     1      12.191  -1.617   1.181  1.00  0.00           O  
HETATM   77  O18 UNL     1      14.357  -1.407   1.842  1.00  0.00           O  
HETATM   78  H1  UNL     1       4.356   0.851   2.811  1.00  0.00           H  
HETATM   79  H2  UNL     1       4.287   1.797   1.321  1.00  0.00           H  
HETATM   80  H3  UNL     1       4.936   2.603   2.780  1.00  0.00           H  
HETATM   81  H4  UNL     1       6.924   2.084   1.845  1.00  0.00           H  
HETATM   82  H5  UNL     1       7.485   0.689   3.286  1.00  0.00           H  
HETATM   83  H6  UNL     1       5.774   1.247  -0.256  1.00  0.00           H  
HETATM   84  H7  UNL     1       4.928  -0.914   1.417  1.00  0.00           H  
HETATM   85  H8  UNL     1       4.546  -3.336  -1.038  1.00  0.00           H  
HETATM   86  H9  UNL     1       3.203  -2.234  -1.427  1.00  0.00           H  
HETATM   87  H10 UNL     1       3.463  -3.595   1.039  1.00  0.00           H  
HETATM   88  H11 UNL     1       2.034  -0.934   2.969  1.00  0.00           H  
HETATM   89  H12 UNL     1      -0.380  -1.693   2.983  1.00  0.00           H  
HETATM   90  H13 UNL     1      -2.127   0.280   1.131  1.00  0.00           H  
HETATM   91  H14 UNL     1      -2.147  -0.769   3.164  1.00  0.00           H  
HETATM   92  H15 UNL     1      -2.334  -2.415   2.501  1.00  0.00           H  
HETATM   93  H16 UNL     1      -4.582  -1.485   1.467  1.00  0.00           H  
HETATM   94  H17 UNL     1      -4.247  -0.019   2.428  1.00  0.00           H  
HETATM   95  H18 UNL     1      -6.520  -2.354   4.263  1.00  0.00           H  
HETATM   96  H19 UNL     1      -2.225  -2.365  -0.336  1.00  0.00           H  
HETATM   97  H20 UNL     1      -3.346  -2.732  -2.021  1.00  0.00           H  
HETATM   98  H21 UNL     1      -2.707  -1.142  -3.691  1.00  0.00           H  
HETATM   99  H22 UNL     1      -4.362  -0.338  -3.551  1.00  0.00           H  
HETATM  100  H23 UNL     1      -3.626  -2.999  -4.729  1.00  0.00           H  
HETATM  101  H24 UNL     1      -5.133  -2.015  -4.972  1.00  0.00           H  
HETATM  102  H25 UNL     1      -5.788  -3.985  -3.477  1.00  0.00           H  
HETATM  103  H26 UNL     1      -4.225  -3.909  -2.695  1.00  0.00           H  
HETATM  104  H27 UNL     1      -8.048  -2.917  -0.734  1.00  0.00           H  
HETATM  105  H28 UNL     1      -7.752  -4.241  -2.499  1.00  0.00           H  
HETATM  106  H29 UNL     1      -9.359  -3.565  -2.645  1.00  0.00           H  
HETATM  107  H30 UNL     1      -8.639  -1.267  -5.162  1.00  0.00           H  
HETATM  108  H31 UNL     1      -9.682  -1.810  -2.549  1.00  0.00           H  
HETATM  109  H32 UNL     1      -9.057   0.700   0.319  1.00  0.00           H  
HETATM  110  H33 UNL     1     -12.078   0.210   0.151  1.00  0.00           H  
HETATM  111  H34 UNL     1     -10.985  -0.899   1.012  1.00  0.00           H  
HETATM  112  H35 UNL     1     -10.004  -0.057   3.144  1.00  0.00           H  
HETATM  113  H36 UNL     1     -10.235   1.511   5.018  1.00  0.00           H  
HETATM  114  H37 UNL     1     -11.073   4.528   5.224  1.00  0.00           H  
HETATM  115  H38 UNL     1     -12.844   3.985   2.796  1.00  0.00           H  
HETATM  116  H39 UNL     1     -12.643   2.452   0.921  1.00  0.00           H  
HETATM  117  H40 UNL     1     -11.394   1.796  -1.314  1.00  0.00           H  
HETATM  118  H41 UNL     1     -10.724   5.097  -0.317  1.00  0.00           H  
HETATM  119  H42 UNL     1      -9.721   4.925  -1.781  1.00  0.00           H  
HETATM  120  H43 UNL     1     -11.512   3.389  -2.541  1.00  0.00           H  
HETATM  121  H44 UNL     1     -12.415   3.866  -1.159  1.00  0.00           H  
HETATM  122  H45 UNL     1     -11.983   4.995  -2.383  1.00  0.00           H  
HETATM  123  H46 UNL     1       1.355  -3.917   2.470  1.00  0.00           H  
HETATM  124  H47 UNL     1       3.248  -3.430   4.632  1.00  0.00           H  
HETATM  125  H48 UNL     1       3.986  -2.827   3.100  1.00  0.00           H  
HETATM  126  H49 UNL     1       3.345  -4.501   3.247  1.00  0.00           H  
HETATM  127  H50 UNL     1       1.078  -3.866   4.703  1.00  0.00           H  
HETATM  128  H51 UNL     1       8.338   2.113  -0.089  1.00  0.00           H  
HETATM  129  H52 UNL     1       9.708  -0.061  -1.576  1.00  0.00           H  
HETATM  130  H53 UNL     1       9.810   3.027  -1.382  1.00  0.00           H  
HETATM  131  H54 UNL     1       9.138   1.984  -2.650  1.00  0.00           H  
HETATM  132  H55 UNL     1      10.825   1.159  -4.556  1.00  0.00           H  
HETATM  133  H56 UNL     1      13.235   1.842  -5.186  1.00  0.00           H  
HETATM  134  H57 UNL     1      15.296   3.227  -4.047  1.00  0.00           H  
HETATM  135  H58 UNL     1      15.877   4.466  -1.961  1.00  0.00           H  
HETATM  136  H59 UNL     1      14.290   4.640  -0.138  1.00  0.00           H  
HETATM  137  H60 UNL     1      11.998   3.571  -0.351  1.00  0.00           H  
HETATM  138  H61 UNL     1      12.217   0.166  -1.686  1.00  0.00           H  
HETATM  139  H62 UNL     1      13.715   1.022   0.713  1.00  0.00           H  
HETATM  140  H63 UNL     1      14.255  -0.078  -0.567  1.00  0.00           H  
HETATM  141  H64 UNL     1      14.593  -0.841   2.640  1.00  0.00           H  
CONECT    1    2   78   79   80
CONECT    2    3    4   81
CONECT    3   82
CONECT    4    5   57   83
CONECT    5    6   84
CONECT    6    7    7    8
CONECT    8    9   85   86
CONECT    9   10   87
CONECT   10   11   11   12
CONECT   12   13   54   88
CONECT   13   14   89
CONECT   14   15   15   16
CONECT   16   17   22   90
CONECT   17   18   91   92
CONECT   18   19   93   94
CONECT   19   20   20   21
CONECT   21   95
CONECT   22   23   96
CONECT   23   24   24   25
CONECT   25   26   29   97
CONECT   26   27   98   99
CONECT   27   28  100  101
CONECT   28   29  102  103
CONECT   29   30
CONECT   30   31   31   32
CONECT   32   33   37  104
CONECT   33   34  105  106
CONECT   34   35   35   36
CONECT   36  107
CONECT   37   38  108
CONECT   38   39   39   40
CONECT   40   41   49  109
CONECT   41   42  110  111
CONECT   42   43   43   48
CONECT   43   44  112
CONECT   44   45   45  113
CONECT   45   46   47
CONECT   46  114
CONECT   47   48   48  115
CONECT   48  116
CONECT   49   50  117
CONECT   50   51   51   52
CONECT   52   53  118  119
CONECT   53  120  121  122
CONECT   54   55   56  123
CONECT   55  124  125  126
CONECT   56  127
CONECT   57   58   58   59
CONECT   59   60  128
CONECT   60   61   71  129
CONECT   61   62  130  131
CONECT   62   63   63   70
CONECT   63   64  132
CONECT   64   65  133
CONECT   65   66   66   70
CONECT   66   67  134
CONECT   67   68   68  135
CONECT   68   69  136
CONECT   69   70   70  137
CONECT   71   72   72   73
CONECT   73   74  138
CONECT   74   75  139  140
CONECT   75   76   76   77
CONECT   77  141
END
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SMILES for HMDB0039422 (Graecunin D)

C[C@@H](O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](CCC(O)=O)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(O)=O)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)C[NH3+])[C@@H](C)O)C(=O)N[C@@H](CC1=CNC2=CC=CC=C12)C(=O)NCC(O)=O
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INCHI for HMDB0039422 (Graecunin D)

InChI=1S/C48H63N11O18/c1-23(60)40(46(75)51-21-36(64)57-41(24(2)61)47(76)55-32(42(71)52-22-39(69)70)17-26-20-50-29-7-4-3-6-28(26)29)58-43(72)30(13-14-37(65)66)54-45(74)34-8-5-15-59(34)48(77)33(18-38(67)68)56-44(73)31(53-35(63)19-49)16-25-9-11-27(62)12-10-25/h3-4,6-7,9-12,20,23-24,30-34,40-41,50,60-62H,5,8,13-19,21-22,49H2,1-2H3,(H,51,75)(H,52,71)(H,53,63)(H,54,74)(H,55,76)(H,56,73)(H,57,64)(H,58,72)(H,65,66)(H,67,68)(H,69,70)/p+1/t23-,24-,30+,31+,32+,33+,34+,40+,41+/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(4S)-4-({[(2S)-1-[(2S)-2-{[(2S)-2-[(2-azaniumyl-1-hydroxyethylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}-3-carboxypropanoyl]pyrrolidin-2-yl](hydroxy)methylidene}amino)-4-{[(1S,2R)-1-[({[(1S,2R)-1-{[(1S)-1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(1H-indol-3-yl)ethyl]-C-hydroxycarbonimidoyl}-2-hydroxypropyl]-C-hydroxycarbonimidoyl}methyl)-C-hydroxycarbonimidoyl]-2-hydroxypropyl]-C-hydroxycarbonimidoyl}butanoateHMDB
Chemical FormulaC48H64N11O18
Average Molecular Weight1083.0847
Monoisotopic Molecular Weight1082.443079299
IUPAC Name(4S)-4-{[(2S)-1-[(2S)-2-[(2S)-2-(2-azaniumylacetamido)-3-(4-hydroxyphenyl)propanamido]-3-carboxypropanoyl]pyrrolidin-2-yl]formamido}-4-{[(1S,2R)-1-[({[(1S,2R)-1-{[(1S)-1-[(carboxymethyl)carbamoyl]-2-(1H-indol-3-yl)ethyl]carbamoyl}-2-hydroxypropyl]carbamoyl}methyl)carbamoyl]-2-hydroxypropyl]carbamoyl}butanoic acid
Traditional Name(4S)-4-{[(2S)-1-[(2S)-2-[(2S)-2-(2-ammonioacetamido)-3-(4-hydroxyphenyl)propanamido]-3-carboxypropanoyl]pyrrolidin-2-yl]formamido}-4-{[(1S,2R)-1-[({[(1S,2R)-1-{[(1S)-1-(carboxymethylcarbamoyl)-2-(1H-indol-3-yl)ethyl]carbamoyl}-2-hydroxypropyl]carbamoyl}methyl)carbamoyl]-2-hydroxypropyl]carbamoyl}butanoic acid
CAS Registry Number74350-29-1
SMILES
C[C@@H](O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](CCC(O)=O)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(O)=O)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)C[NH3+])[C@@H](C)O)C(=O)N[C@@H](CC1=CNC2=CC=CC=C12)C(=O)NCC(O)=O
InChI Identifier
InChI=1S/C48H63N11O18/c1-23(60)40(46(75)51-21-36(64)57-41(24(2)61)47(76)55-32(42(71)52-22-39(69)70)17-26-20-50-29-7-4-3-6-28(26)29)58-43(72)30(13-14-37(65)66)54-45(74)34-8-5-15-59(34)48(77)33(18-38(67)68)56-44(73)31(53-35(63)19-49)16-25-9-11-27(62)12-10-25/h3-4,6-7,9-12,20,23-24,30-34,40-41,50,60-62H,5,8,13-19,21-22,49H2,1-2H3,(H,51,75)(H,52,71)(H,53,63)(H,54,74)(H,55,76)(H,56,73)(H,57,64)(H,58,72)(H,65,66)(H,67,68)(H,69,70)/p+1/t23-,24-,30+,31+,32+,33+,34+,40+,41+/m1/s1
InChI KeyYYYJTUAEGPSBSQ-GZCAAYOFSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentOligopeptides
Alternative Parents
Substituents
  • Alpha-oligopeptide
  • Tyrosine or derivatives
  • Phenylalanine or derivatives
  • Glutamic acid or derivatives
  • Proline or derivatives
  • N-acyl-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid amide
  • Triptan
  • N-substituted-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Amphetamine or derivatives
  • 3-alkylindole
  • Indole
  • Indole or derivatives
  • Tricarboxylic acid or derivatives
  • N-acylpyrrolidine
  • Pyrrolidine carboxylic acid or derivatives
  • Pyrrolidine-2-carboxamide
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Fatty acyl
  • Fatty amide
  • Substituted pyrrole
  • N-acyl-amine
  • Benzenoid
  • Monocyclic benzene moiety
  • Tertiary carboxylic acid amide
  • Heteroaromatic compound
  • Pyrrolidine
  • Pyrrole
  • Amino acid
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Amino acid or derivatives
  • Carboxamide group
  • Carboxylic acid
  • Organoheterocyclic compound
  • Azacycle
  • Organic nitrogen compound
  • Primary amine
  • Organic oxide
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organonitrogen compound
  • Organopnictogen compound
  • Organooxygen compound
  • Amine
  • Organic oxygen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point141 - 142 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.049 g/LALOGPS
logP-1.1ALOGPS
logP-8.6ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)3.11ChemAxon
pKa (Strongest Basic)7.83ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area469.13 ŲChemAxon
Rotatable Bond Count29ChemAxon
Refractivity272.73 m³·mol⁻¹ChemAxon
Polarizability105.37 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-333.0430932474
DeepCCS[M+Na]+306.97630932474
AllCCS[M+H]+307.332859911
AllCCS[M+H-H2O]+308.132859911
AllCCS[M+NH4]+306.432859911
AllCCS[M+Na]+306.232859911
AllCCS[M-H]-307.132859911
AllCCS[M+Na-2H]-312.432859911
AllCCS[M+HCOO]-318.132859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 10V, Positive-QTOFsplash10-0f89-9400000000-9cb73fbd7f5d345aae782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 20V, Positive-QTOFsplash10-0089-9100000000-1a6ce3717f9c678a0d372016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 40V, Positive-QTOFsplash10-00ai-9000000000-7aae9b9fe9ee782dfcb92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 10V, Negative-QTOFsplash10-001i-9200000000-7a56239cca7e202e665b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 20V, Negative-QTOFsplash10-0fl0-9200000000-2bff1e470700947178782016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 40V, Negative-QTOFsplash10-00di-9000000000-481326004e41370148572016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 10V, Positive-QTOFsplash10-03dr-9100242000-0ef43198063c628106612021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 20V, Positive-QTOFsplash10-000i-4332397005-f10d89139a1ca5180ae62021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Graecunin D 40V, Positive-QTOFsplash10-053i-1910141001-75be6c6f1e641f09915b2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB019006
KNApSAcK IDNot Available
Chemspider ID3571924
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound4369318
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .