Hmdb loader

Showing metabocard for Crocin 3 (HMDB0039121)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:29:16 UTC
Update Date2022-03-07 02:56:05 UTC
HMDB IDHMDB0039121
Secondary Accession Numbers
  • HMDB39121
Metabolite Identification
Common NameCrocin 3
DescriptionCrocin 3 belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review a significant number of articles have been published on Crocin 3.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0039121 (Crocin 3)

  Mrv0541 05061310522D          

 46 47  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0039121 (Crocin 3)

HMDB0039121
     RDKit          3D
Crocin 3
 90 91  0  0  0  0  0  0  0  0999 V2000
    4.1636    1.0907    4.7764 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.9151    0.6386    3.2022 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4073    0.2508    1.8822 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7344    0.2106    1.6700 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2474   -0.1707    0.3683 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5400   -0.2320    0.0746 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4723    0.1120    1.1612 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0039121 (Crocin 3)

  Mrv0541 05061310522D          

 46 47  0  0  0  0            999 V2000
    0.0000  -11.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579  -14.0250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289  -12.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289  -11.5500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289  -12.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145  -12.7875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434  -11.1375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145  -12.7875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434  -12.7875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000  -12.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434  -13.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289  -14.0250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289  -14.8500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145  -13.6125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 12  8  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 17  1  1  0  0  0  0
 17  9  2  0  0  0  0
 17 11  1  0  0  0  0
 18  2  1  0  0  0  0
 18 10  2  0  0  0  0
 18 12  1  0  0  0  0
 19  3  1  0  0  0  0
 19 13  2  0  0  0  0
 20  4  1  0  0  0  0
 20 14  2  0  0  0  0
 21 15  1  0  0  0  0
 22 16  1  0  0  0  0
 23 21  1  0  0  0  0
 24 22  1  0  0  0  0
 25 23  1  0  0  0  0
 26 24  1  0  0  0  0
 27 25  1  0  0  0  0
 28 26  1  0  0  0  0
 29 19  1  0  0  0  0
 30 20  1  0  0  0  0
 31 27  1  0  0  0  0
 32 28  1  0  0  0  0
 33 15  1  0  0  0  0
 34 23  1  0  0  0  0
 35 24  1  0  0  0  0
 36 25  1  0  0  0  0
 37 26  1  0  0  0  0
 38 27  1  0  0  0  0
 39 28  1  0  0  0  0
 40 29  2  0  0  0  0
 41 29  1  0  0  0  0
 42 30  2  0  0  0  0
 43 16  1  0  0  0  0
 43 31  1  0  0  0  0
 44 21  1  0  0  0  0
 44 31  1  0  0  0  0
 45 22  1  0  0  0  0
 45 32  1  0  0  0  0
 46 30  1  0  0  0  0
 46 32  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0039121

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C(\C=C\C=C(\C)C(O)=O)=C/C=C/C=C(/C)\C=C\C=C(/C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C32H44O14/c1-17(11-7-13-19(3)29(40)41)9-5-6-10-18(2)12-8-14-20(4)30(42)46-32-28(39)26(37)24(35)22(45-32)16-43-31-27(38)25(36)23(34)21(15-33)44-31/h5-14,21-28,31-39H,15-16H2,1-4H3,(H,40,41)/b6-5+,11-7+,12-8+,17-9+,18-10-,19-13-,20-14+

> <INCHI_KEY>
VULLCGFNYWDRHL-BCMXLCDNSA-N

> <FORMULA>
C32H44O14

> <MOLECULAR_WEIGHT>
652.6834

> <EXACT_MASS>
652.273106116

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
69.76935764020601

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethyl-16-oxo-16-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoic acid

> <ALOGPS_LOGP>
1.70

> <JCHEM_LOGP>
0.5946328250000007

> <ALOGPS_LOGS>
-3.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.903052250054039

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.946209426053647

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083422322401

> <JCHEM_POLAR_SURFACE_AREA>
232.89999999999995

> <JCHEM_REFRACTIVITY>
168.64130000000011

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.91e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethyl-16-oxo-16-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0039121 (Crocin 3)

HMDB0039121
     RDKit          3D
Crocin 3
 90 91  0  0  0  0  0  0  0  0999 V2000
    4.1636    1.0907    4.7764 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6222    0.6872    3.4053 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9151    0.6386    3.2022 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4073    0.2508    1.8822 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7344    0.2106    1.6700 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2474   -0.1707    0.3683 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5400   -0.2320    0.0746 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4723    0.1120    1.1612 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0016   -0.6022   -1.2420 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2590   -0.6878   -1.6277 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6040   -1.0751   -3.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8032   -1.1868   -3.4707 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9260   -1.5968   -4.9113 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9676   -0.9344   -2.6558 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9232   -0.6034   -1.4715 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2119   -1.0897   -3.3018 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6557    0.3645    2.3946 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3548    0.4629    2.7056 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3236    0.1447    1.7164 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0372    0.2501    2.0029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2847    0.7097    3.3786 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0378   -0.0620    1.0673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7796   -0.4771   -0.0870 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3381    0.1145    1.4881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4097   -0.1894    0.5823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9785    1.0307    0.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2964    1.0670   -0.0154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6693    0.3869   -1.3462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8725    0.4933   -1.6096 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0892    0.6004   -1.8750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5766   -0.1574   -2.9896 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8945   -0.5058   -2.7689 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0878   -1.8514   -2.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4908   -1.9838   -0.8796 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6653    0.5121   -1.9437 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0407    0.4695   -2.3183 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1456    1.8629   -2.3096 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3158    1.9753   -3.7133 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6807    1.9979   -2.0261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5801    2.6828   -0.7959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1715    0.4907    1.0994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4856    1.5471    1.9876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5016   -0.5683    1.9029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4327   -1.6191    2.0817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2883   -1.1650    1.2766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5783   -1.7958    2.3353 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6250    0.2163    5.1942 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0030    1.3141    5.4385 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4531    1.9624    4.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6375    0.8817    4.0041 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8079   -0.0090    1.0478 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3915    0.4691    2.4838 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5509   -0.4201   -0.4118 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1837   -0.4435    2.0946 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5242   -0.1469    0.9823 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4656    1.2239    1.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2424   -0.8365   -1.9946 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9809   -0.4537   -0.8713 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7593   -1.2866   -3.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5511   -0.7371   -5.5112 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2245   -2.4348   -5.0945 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9788   -1.8353   -5.1684 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0631   -0.9243   -2.7589 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8431    0.0451    1.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0388    0.7739    3.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6025   -0.1863    0.7367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3947    0.8690    3.4951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0297   -0.0455    4.1571 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1815    1.6829    3.5541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9304   -0.5883   -0.3416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6006    2.1303   -0.1172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3661   -0.7069   -1.1280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8709    0.6506   -2.1085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7288    0.1596   -1.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3805   -0.5949   -3.7936 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1912   -1.9954   -1.9358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7791   -2.6550   -2.8222 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0721   -1.6243   -0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6848    0.2856   -0.8647 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4846   -0.3110   -1.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7411    2.6816   -1.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4341    1.9629   -4.1769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2215    2.5808   -2.8239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5248    2.0033   -0.0722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1388    0.1521    0.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2408    2.4106    1.5435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2428   -0.2330    2.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9434   -1.4503    2.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6053   -2.0335    0.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9807   -1.6444    3.2041 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
 14 16  1  0
  2 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 32 35  1  0
 35 36  1  0
 35 37  1  0
 37 38  1  0
 37 39  1  0
 39 40  1  0
 27 41  1  0
 41 42  1  0
 41 43  1  0
 43 44  1  0
 43 45  1  0
 45 46  1  0
 45 25  1  0
 39 30  1  0
  1 47  1  0
  1 48  1  0
  1 49  1  0
  3 50  1  0
  4 51  1  0
  5 52  1  0
  6 53  1  0
  8 54  1  0
  8 55  1  0
  8 56  1  0
  9 57  1  0
 10 58  1  0
 11 59  1  0
 13 60  1  0
 13 61  1  0
 13 62  1  0
 16 63  1  0
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 18 65  1  0
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 21 67  1  0
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 25 70  1  0
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 32 75  1  0
 33 76  1  0
 33 77  1  0
 34 78  1  0
 35 79  1  0
 36 80  1  0
 37 81  1  0
 38 82  1  0
 39 83  1  0
 40 84  1  0
 41 85  1  0
 42 86  1  0
 43 87  1  0
 44 88  1  0
 45 89  1  0
 46 90  1  0
M  END
Download

PDB for HMDB0039121 (Crocin 3)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       0.000 -21.560   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335 -18.480   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.335 -26.180   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667 -13.860   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667 -23.100   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667 -21.560   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667 -23.100   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667 -16.940   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334 -23.870   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001 -20.790   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334 -23.870   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667 -18.480   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001 -23.870   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334 -16.170   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000 -23.100   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001 -19.250   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.001 -25.410   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334 -14.630   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.667 -26.180   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000 -13.860   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -5.335 -12.320   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -2.667 -27.720   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -1.334 -25.410   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -1.334 -14.630   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       0.000 -12.320   0.000  0.00  0.00           O+0
CONECT    1   17                                                            
CONECT    2   18                                                            
CONECT    3   19                                                            
CONECT    4   20                                                            
CONECT    5    6    9                                                       
CONECT    6    5   10                                                       
CONECT    7   11   13                                                       
CONECT    8   12   14                                                       
CONECT    9    5   17                                                       
CONECT   10    6   18                                                       
CONECT   11    7   17                                                       
CONECT   12    8   18                                                       
CONECT   13    7   19                                                       
CONECT   14    8   20                                                       
CONECT   15   21   33                                                       
CONECT   16   22   43                                                       
CONECT   17    1    9   11                                                  
CONECT   18    2   10   12                                                  
CONECT   19    3   13   29                                                  
CONECT   20    4   14   30                                                  
CONECT   21   15   23   44                                                  
CONECT   22   16   24   45                                                  
CONECT   23   21   25   34                                                  
CONECT   24   22   26   35                                                  
CONECT   25   23   27   36                                                  
CONECT   26   24   28   37                                                  
CONECT   27   25   31   38                                                  
CONECT   28   26   32   39                                                  
CONECT   29   19   40   41                                                  
CONECT   30   20   42   46                                                  
CONECT   31   27   43   44                                                  
CONECT   32   28   45   46                                                  
CONECT   33   15                                                            
CONECT   34   23                                                            
CONECT   35   24                                                            
CONECT   36   25                                                            
CONECT   37   26                                                            
CONECT   38   27                                                            
CONECT   39   28                                                            
CONECT   40   29                                                            
CONECT   41   29                                                            
CONECT   42   30                                                            
CONECT   43   16   31                                                       
CONECT   44   21   31                                                       
CONECT   45   22   32                                                       
CONECT   46   30   32                                                       
MASTER        0    0    0    0    0    0    0    0   46    0   94    0
END
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3D PDB for HMDB0039121 (Crocin 3)

COMPND    HMDB0039121
HETATM    1  C1  UNL     1       4.164   1.091   4.776  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.622   0.687   3.405  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.915   0.639   3.202  1.00  0.00           C  
HETATM    4  C4  UNL     1       6.407   0.251   1.882  1.00  0.00           C  
HETATM    5  C5  UNL     1       7.734   0.211   1.670  1.00  0.00           C  
HETATM    6  C6  UNL     1       8.247  -0.171   0.368  1.00  0.00           C  
HETATM    7  C7  UNL     1       9.540  -0.232   0.075  1.00  0.00           C  
HETATM    8  C8  UNL     1      10.472   0.112   1.161  1.00  0.00           C  
HETATM    9  C9  UNL     1      10.002  -0.602  -1.242  1.00  0.00           C  
HETATM   10  C10 UNL     1      11.259  -0.688  -1.628  1.00  0.00           C  
HETATM   11  C11 UNL     1      11.604  -1.075  -3.000  1.00  0.00           C  
HETATM   12  C12 UNL     1      12.803  -1.187  -3.471  1.00  0.00           C  
HETATM   13  C13 UNL     1      12.926  -1.597  -4.911  1.00  0.00           C  
HETATM   14  C14 UNL     1      13.968  -0.934  -2.656  1.00  0.00           C  
HETATM   15  O1  UNL     1      13.923  -0.603  -1.472  1.00  0.00           O  
HETATM   16  O2  UNL     1      15.212  -1.090  -3.302  1.00  0.00           O  
HETATM   17  C15 UNL     1       3.656   0.365   2.395  1.00  0.00           C  
HETATM   18  C16 UNL     1       2.355   0.463   2.706  1.00  0.00           C  
HETATM   19  C17 UNL     1       1.324   0.145   1.716  1.00  0.00           C  
HETATM   20  C18 UNL     1       0.037   0.250   2.003  1.00  0.00           C  
HETATM   21  C19 UNL     1      -0.285   0.710   3.379  1.00  0.00           C  
HETATM   22  C20 UNL     1      -1.038  -0.062   1.067  1.00  0.00           C  
HETATM   23  O3  UNL     1      -0.780  -0.477  -0.087  1.00  0.00           O  
HETATM   24  O4  UNL     1      -2.338   0.115   1.488  1.00  0.00           O  
HETATM   25  C21 UNL     1      -3.410  -0.189   0.582  1.00  0.00           C  
HETATM   26  O5  UNL     1      -3.979   1.031   0.283  1.00  0.00           O  
HETATM   27  C22 UNL     1      -5.296   1.067  -0.015  1.00  0.00           C  
HETATM   28  C23 UNL     1      -5.669   0.387  -1.346  1.00  0.00           C  
HETATM   29  O6  UNL     1      -6.872   0.493  -1.610  1.00  0.00           O  
HETATM   30  C24 UNL     1      -8.089   0.600  -1.875  1.00  0.00           C  
HETATM   31  O7  UNL     1      -8.577  -0.157  -2.990  1.00  0.00           O  
HETATM   32  C25 UNL     1      -9.894  -0.506  -2.769  1.00  0.00           C  
HETATM   33  C26 UNL     1     -10.088  -1.851  -2.126  1.00  0.00           C  
HETATM   34  O8  UNL     1      -9.491  -1.984  -0.880  1.00  0.00           O  
HETATM   35  C27 UNL     1     -10.665   0.512  -1.944  1.00  0.00           C  
HETATM   36  O9  UNL     1     -12.041   0.469  -2.318  1.00  0.00           O  
HETATM   37  C28 UNL     1     -10.146   1.863  -2.310  1.00  0.00           C  
HETATM   38  O10 UNL     1     -10.316   1.975  -3.713  1.00  0.00           O  
HETATM   39  C29 UNL     1      -8.681   1.998  -2.026  1.00  0.00           C  
HETATM   40  O11 UNL     1      -8.580   2.683  -0.796  1.00  0.00           O  
HETATM   41  C30 UNL     1      -6.172   0.491   1.099  1.00  0.00           C  
HETATM   42  O12 UNL     1      -6.486   1.547   1.988  1.00  0.00           O  
HETATM   43  C31 UNL     1      -5.502  -0.568   1.903  1.00  0.00           C  
HETATM   44  O13 UNL     1      -6.433  -1.619   2.082  1.00  0.00           O  
HETATM   45  C32 UNL     1      -4.288  -1.165   1.277  1.00  0.00           C  
HETATM   46  O14 UNL     1      -3.578  -1.796   2.335  1.00  0.00           O  
HETATM   47  H1  UNL     1       3.625   0.216   5.194  1.00  0.00           H  
HETATM   48  H2  UNL     1       5.003   1.314   5.438  1.00  0.00           H  
HETATM   49  H3  UNL     1       3.453   1.962   4.692  1.00  0.00           H  
HETATM   50  H4  UNL     1       6.638   0.882   4.004  1.00  0.00           H  
HETATM   51  H5  UNL     1       5.808  -0.009   1.048  1.00  0.00           H  
HETATM   52  H6  UNL     1       8.391   0.469   2.484  1.00  0.00           H  
HETATM   53  H7  UNL     1       7.551  -0.420  -0.412  1.00  0.00           H  
HETATM   54  H8  UNL     1      10.184  -0.444   2.095  1.00  0.00           H  
HETATM   55  H9  UNL     1      11.524  -0.147   0.982  1.00  0.00           H  
HETATM   56  H10 UNL     1      10.466   1.224   1.374  1.00  0.00           H  
HETATM   57  H11 UNL     1       9.242  -0.837  -1.995  1.00  0.00           H  
HETATM   58  H12 UNL     1      11.981  -0.454  -0.871  1.00  0.00           H  
HETATM   59  H13 UNL     1      10.759  -1.287  -3.683  1.00  0.00           H  
HETATM   60  H14 UNL     1      12.551  -0.737  -5.511  1.00  0.00           H  
HETATM   61  H15 UNL     1      12.225  -2.435  -5.095  1.00  0.00           H  
HETATM   62  H16 UNL     1      13.979  -1.835  -5.168  1.00  0.00           H  
HETATM   63  H17 UNL     1      16.063  -0.924  -2.759  1.00  0.00           H  
HETATM   64  H18 UNL     1       3.843   0.045   1.391  1.00  0.00           H  
HETATM   65  H19 UNL     1       2.039   0.774   3.689  1.00  0.00           H  
HETATM   66  H20 UNL     1       1.602  -0.186   0.737  1.00  0.00           H  
HETATM   67  H21 UNL     1      -1.395   0.869   3.495  1.00  0.00           H  
HETATM   68  H22 UNL     1      -0.030  -0.046   4.157  1.00  0.00           H  
HETATM   69  H23 UNL     1       0.182   1.683   3.554  1.00  0.00           H  
HETATM   70  H24 UNL     1      -2.930  -0.588  -0.342  1.00  0.00           H  
HETATM   71  H25 UNL     1      -5.601   2.130  -0.117  1.00  0.00           H  
HETATM   72  H26 UNL     1      -5.366  -0.707  -1.128  1.00  0.00           H  
HETATM   73  H27 UNL     1      -4.871   0.651  -2.109  1.00  0.00           H  
HETATM   74  H28 UNL     1      -8.729   0.160  -1.030  1.00  0.00           H  
HETATM   75  H29 UNL     1     -10.380  -0.595  -3.794  1.00  0.00           H  
HETATM   76  H30 UNL     1     -11.191  -1.995  -1.936  1.00  0.00           H  
HETATM   77  H31 UNL     1      -9.779  -2.655  -2.822  1.00  0.00           H  
HETATM   78  H32 UNL     1     -10.072  -1.624  -0.161  1.00  0.00           H  
HETATM   79  H33 UNL     1     -10.685   0.286  -0.865  1.00  0.00           H  
HETATM   80  H34 UNL     1     -12.485  -0.311  -1.899  1.00  0.00           H  
HETATM   81  H35 UNL     1     -10.741   2.682  -1.827  1.00  0.00           H  
HETATM   82  H36 UNL     1      -9.434   1.963  -4.177  1.00  0.00           H  
HETATM   83  H37 UNL     1      -8.222   2.581  -2.824  1.00  0.00           H  
HETATM   84  H38 UNL     1      -8.525   2.003  -0.072  1.00  0.00           H  
HETATM   85  H39 UNL     1      -7.139   0.152   0.682  1.00  0.00           H  
HETATM   86  H40 UNL     1      -6.241   2.411   1.543  1.00  0.00           H  
HETATM   87  H41 UNL     1      -5.243  -0.233   2.933  1.00  0.00           H  
HETATM   88  H42 UNL     1      -6.943  -1.450   2.898  1.00  0.00           H  
HETATM   89  H43 UNL     1      -4.605  -2.033   0.644  1.00  0.00           H  
HETATM   90  H44 UNL     1      -3.981  -1.644   3.204  1.00  0.00           H  
CONECT    1    2   47   48   49
CONECT    2    3    3   17
CONECT    3    4   50
CONECT    4    5    5   51
CONECT    5    6   52
CONECT    6    7    7   53
CONECT    7    8    9
CONECT    8   54   55   56
CONECT    9   10   10   57
CONECT   10   11   58
CONECT   11   12   12   59
CONECT   12   13   14
CONECT   13   60   61   62
CONECT   14   15   15   16
CONECT   16   63
CONECT   17   18   18   64
CONECT   18   19   65
CONECT   19   20   20   66
CONECT   20   21   22
CONECT   21   67   68   69
CONECT   22   23   23   24
CONECT   24   25
CONECT   25   26   45   70
CONECT   26   27
CONECT   27   28   41   71
CONECT   28   29   72   73
CONECT   29   30
CONECT   30   31   39   74
CONECT   31   32
CONECT   32   33   35   75
CONECT   33   34   76   77
CONECT   34   78
CONECT   35   36   37   79
CONECT   36   80
CONECT   37   38   39   81
CONECT   38   82
CONECT   39   40   83
CONECT   40   84
CONECT   41   42   43   85
CONECT   42   86
CONECT   43   44   45   87
CONECT   44   88
CONECT   45   46   89
CONECT   46   90
END
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SMILES for HMDB0039121 (Crocin 3)

C\C(\C=C\C=C(\C)C(O)=O)=C/C=C/C=C(/C)\C=C\C=C(/C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O
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INCHI for HMDB0039121 (Crocin 3)

InChI=1S/C32H44O14/c1-17(11-7-13-19(3)29(40)41)9-5-6-10-18(2)12-8-14-20(4)30(42)46-32-28(39)26(37)24(35)22(45-32)16-43-31-27(38)25(36)23(34)21(15-33)44-31/h5-14,21-28,31-39H,15-16H2,1-4H3,(H,40,41)/b6-5+,11-7+,12-8+,17-9+,18-10-,19-13-,20-14+
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(2Z,6E,8E,10Z,12E,14E)-2,6,11,15-Tetramethyl-16-oxo-16-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoateHMDB
Chemical FormulaC32H44O14
Average Molecular Weight652.6834
Monoisotopic Molecular Weight652.273106116
IUPAC Name(2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethyl-16-oxo-16-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoic acid
Traditional Name(2Z,4E,6E,8E,10Z,12E,14E)-2,6,11,15-tetramethyl-16-oxo-16-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}hexadeca-2,4,6,8,10,12,14-heptaenoic acid
CAS Registry Number55750-85-1
SMILES
C\C(\C=C\C=C(\C)C(O)=O)=C/C=C/C=C(/C)\C=C\C=C(/C)C(=O)OC1OC(COC2OC(CO)C(O)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C32H44O14/c1-17(11-7-13-19(3)29(40)41)9-5-6-10-18(2)12-8-14-20(4)30(42)46-32-28(39)26(37)24(35)22(45-32)16-43-31-27(38)25(36)23(34)21(15-33)44-31/h5-14,21-28,31-39H,15-16H2,1-4H3,(H,40,41)/b6-5+,11-7+,12-8+,17-9+,18-10-,19-13-,20-14+
InChI KeyVULLCGFNYWDRHL-BCMXLCDNSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassDiterpenoids
Direct ParentDiterpenoids
Alternative Parents
Substituents
  • Diterpenoid
  • Saccharolipid
  • Long-chain fatty acid
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Branched fatty acid
  • Fatty acid ester
  • Heterocyclic fatty acid
  • Hydroxy fatty acid
  • Methyl-branched fatty acid
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Unsaturated fatty acid
  • Oxane
  • Enoate ester
  • Alpha,beta-unsaturated carboxylic ester
  • Secondary alcohol
  • Carboxylic acid ester
  • Polyol
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Oxacycle
  • Carboxylic acid
  • Acetal
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organic oxygen compound
  • Primary alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point204 - 208 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility19.51 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
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 IDFDB018631
KNApSAcK IDC00045803
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131752553
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1874391
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.