Hmdb loader

Showing metabocard for YGM 1A (HMDB0035459)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:27:00 UTC
Update Date2022-03-07 02:54:31 UTC
HMDB IDHMDB0035459
Secondary Accession Numbers
  • HMDB35459
Metabolite Identification
Common NameYGM 1A
DescriptionYGM 1A belongs to the class of organic compounds known as anthocyanidin 3-o-6-p-coumaroyl glycosides. These are anthocyanidin 3-O-glycosides where the carbohydrate moiety is esterified at the C6 position with a p-coumaric acid. P-coumaric acid is an organic derivative of cinnamic acid, that carries a hydroxyl group at the 4-position of the benzene ring. YGM 1A has been detected, but not quantified in, root vegetables. This could make YGM 1A a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on YGM 1A.
Structure
Data?1563862723
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035459 (YGM 1A)


  Mrv0541 05061308282D          

 75 82  0  0  0  0            999 V2000
    2.1434    6.1875    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
    9.2881    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    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
    5.0013   -1.2375    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    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
    7.1447    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    5.7750    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
    2.1434   -0.4125    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
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    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.7171    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579   -1.6500    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
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    6.4302    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  3  2  0  0  0  0
  7  4  2  0  0  0  0
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 10  2  2  0  0  0  0
 19  1  1  0  0  0  0
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 20  3  1  0  0  0  0
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 74 33  1  0  0  0  0
 74 49  1  0  0  0  0
 75 45  1  0  0  0  0
 75 48  1  0  0  0  0
M  CHG  1  69   1
M  END
Download

3D MOL for HMDB0035459 (YGM 1A)

HMDB0035459
     RDKit          3D
YGM 1A
126133  0  0  0  0  0  0  0  0999 V2000
   -9.7610    2.3049   -0.7381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8210    1.6213   -1.2549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2205    0.4867   -2.0824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2244   -0.2418   -2.6335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8402    0.0985   -2.4046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8612   -0.6417   -2.9496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2546   -1.7200   -3.7235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5335   -0.3128   -2.7260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5403   -0.7699   -3.5840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1611   -0.2698   -3.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9728   -0.7689   -1.8230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6897   -0.5926   -1.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6488   -1.3481   -0.1936 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3097   -2.2850   -0.0981 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705   -2.3435    1.2624 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1912   -1.0816    1.8444 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3805   -0.4279    1.8692 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4198   -0.9454    1.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6254   -0.2755    1.1304 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6884   -0.7782    0.3601 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4698   -1.9191   -0.3951 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4739   -2.5071   -1.1428 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3099   -2.2607   -2.5316 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6159   -2.2029   -3.0772 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5831   -2.0339   -4.5563 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.5072    0.6899    2.6425 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4725    1.2927    3.4824 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7275    2.5484    4.0601 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.3575    2.5237    5.2573 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.0674   -3.5482    1.9672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2562   -2.8740    2.5933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4068   -1.5520    2.2128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4145   -0.7067    2.5468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3342   -1.1625    3.2719 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7729    3.5731    1.3804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0228    4.9252    1.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1437    5.5576    1.5000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3658    6.9114    1.1931 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.8388    3.5447    2.5276 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4223   -3.9405    0.5521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4711   -3.1828    0.0542 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.4840   -3.9383   -1.6804 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6862    1.6730   -1.6642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2452    3.0159   -1.6949 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1710    1.2371   -3.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.4864    1.2297   -1.5800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4430    1.9913   -1.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2531    0.2336   -2.2566 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  1  38   1
M  END
Download

3D SDF for HMDB0035459 (YGM 1A)


  Mrv0541 05061308282D          

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M  CHG  1  69   1
M  END
> <DATABASE_ID>
HMDB0035459

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(OC2=CC(O)=CC3=[O+]C(=C(OC4OC(COC(=O)\C=C\C5=CC(O)=C(O)C=C5)C(O)C(O)C4OC4OC(COC(O)=C5C=CC(=O)C=C5)C(O)C(O)C4O)C=C23)C2=CC(O)=C(O)C=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C49H50O26/c50-16-32-36(58)39(61)42(64)47(72-32)70-30-14-23(52)13-29-24(30)15-31(44(69-29)21-5-9-26(54)28(56)12-21)71-49-45(41(63)38(60)33(74-49)17-67-35(57)10-2-19-1-8-25(53)27(55)11-19)75-48-43(65)40(62)37(59)34(73-48)18-68-46(66)20-3-6-22(51)7-4-20/h1-15,32-34,36-43,45,47-50,58-65H,16-18H2,(H5-,51,52,53,54,55,56,57,66)/p+1

> <INCHI_KEY>
GLMCQQPCNPVXHL-UHFFFAOYSA-O

> <FORMULA>
C49H51O26

> <MOLECULAR_WEIGHT>
1055.9136

> <EXACT_MASS>
1055.266856804

> <JCHEM_ACCEPTOR_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
101.93200703657187

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
15

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3,4-dihydroxyphenyl)-3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-[(3,4,5-trihydroxy-6-{[hydroxy(4-oxocyclohexa-2,5-dien-1-ylidene)methoxy]methyl}oxan-2-yl)oxy]oxan-2-yl]oxy}-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium

> <ALOGPS_LOGP>
1.69

> <JCHEM_LOGP>
0.6072999999999962

> <ALOGPS_LOGS>
-3.67

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.813496637535619

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.171324775224326

> <JCHEM_PKA_STRONGEST_BASIC>
-3.947772486514805

> <JCHEM_POLAR_SURFACE_AREA>
424.57000000000016

> <JCHEM_REFRACTIVITY>
268.8509000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3,4-dihydroxyphenyl)-3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-[(3,4,5-trihydroxy-6-{[hydroxy(4-oxocyclohexa-2,5-dien-1-ylidene)methoxy]methyl}oxan-2-yl)oxy]oxan-2-yl]oxy}-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035459 (YGM 1A)

HMDB0035459
     RDKit          3D
YGM 1A
126133  0  0  0  0  0  0  0  0999 V2000
   -9.7610    2.3049   -0.7381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8210    1.6213   -1.2549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2205    0.4867   -2.0824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2244   -0.2418   -2.6335 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8402    0.0985   -2.4046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8612   -0.6417   -2.9496 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2546   -1.7200   -3.7235 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5335   -0.3128   -2.7260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5403   -0.7699   -3.5840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1611   -0.2698   -3.0985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9728   -0.7689   -1.8230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6897   -0.5926   -1.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6488   -1.3481   -0.1936 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3097   -2.2850   -0.0981 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705   -2.3435    1.2624 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1912   -1.0816    1.8444 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3805   -0.4279    1.8692 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4198   -0.9454    1.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6254   -0.2755    1.1304 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6884   -0.7782    0.3601 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4698   -1.9191   -0.3951 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4739   -2.5071   -1.1428 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3099   -2.2607   -2.5316 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6159   -2.2029   -3.0772 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5831   -2.0339   -4.5563 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9278   -3.0732   -5.2158 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4339   -3.3720   -2.5974 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0970   -3.8982   -3.7210 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6358   -4.4749   -1.9725 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5399   -5.2319   -1.1983 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5610   -4.0152   -1.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7572   -4.3579    0.2837 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8747   -0.1046    0.4066 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0010    1.0463    1.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2378    1.6729    1.1991 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9428    1.5028    1.9393 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6995    0.8402    1.9218 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7087    1.2910    2.6282 O   0  0  0  0  0  3  0  0  0  0  0  0
    2.5072    0.6899    2.6425 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4725    1.2927    3.4824 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7275    2.5484    4.0601 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    3.1517    4.9227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3575    2.5237    5.2573 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2531    3.1216    6.1240 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6145    1.2978    4.6980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7748    0.6017    4.9746 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3072    0.6911    3.8106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1259   -3.0199    2.1546 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0674   -3.5482    1.9672 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2562   -2.8740    2.5933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4068   -1.5520    2.2128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4145   -0.7067    2.5468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3342   -1.1625    3.2719 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4855    0.7117    2.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4980    1.4649    2.4685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6926    2.8623    2.1149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7729    3.5731    1.3804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0228    4.9252    1.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1437    5.5576    1.5000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3658    6.9114    1.1931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0778    4.8668    2.2360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2542    5.4886    2.6807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8388    3.5447    2.5276 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4223   -3.9405    0.5521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4711   -3.1828    0.0542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2406   -3.7191   -0.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4840   -3.9383   -1.6804 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4755    0.8833   -1.1759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1748    1.2841    0.1016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6862    1.6730   -1.6642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2452    3.0159   -1.6949 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1710    1.2371   -3.0067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4585    1.7688   -4.0809 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4864    1.2297   -1.5800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4430    1.9913   -1.0054 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2531    0.2336   -2.2566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5577   -1.0780   -3.2430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0050   -1.7599   -4.3732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7168   -0.4871   -4.6455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5052   -1.8773   -3.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4021   -0.6682   -3.7760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0249   -0.9251   -2.1172 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1141   -2.1801   -0.8850 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9126   -2.8502    1.2243 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3460   -1.8144    0.4751 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4844   -2.1321   -0.8728 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0537   -1.2806   -2.6276 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5929   -1.9039   -4.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0440   -1.0781   -4.7737 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9515   -2.8046   -6.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2163   -3.0597   -1.8798 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8700   -3.3320   -3.9744 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2377   -5.1979   -2.7276 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8972   -4.7127   -0.4299 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5921   -4.5061   -1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1416   -5.2656    0.3972 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7355   -0.4161   -0.1530 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0231    1.3575    0.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0398    2.3971    2.5528 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6682    3.0232    3.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0604    4.1327    5.3724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1284    2.7485    6.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4859    0.9432    5.5910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0565   -0.2731    3.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0344   -4.5610    2.5212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1719   -2.8626    3.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1924   -3.4838    2.4347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7122    1.1570    1.4961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2521    0.9825    3.0866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8732    3.1318    1.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2913    5.4730    0.5071 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3719    1.2447   -1.8396 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5940    1.9068    0.1390 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.2101    2.8360   -0.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
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 75126  1  0
M  CHG  1  38   1
M  END
Download

PDB for HMDB0035459 (YGM 1A)

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       4.001  11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.338   8.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.004  10.780   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.672   9.240   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.338  11.550   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.004   9.240   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      18.672  10.780   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.334  13.090   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      14.671   3.850   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      14.671   2.310   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      14.671   8.470   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      20.005  11.550   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       2.667  15.400   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       0.000  13.860   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      16.004   4.620   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0       0.000   6.160   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      16.004   1.540   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      13.337   0.000   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      13.337   9.240   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      14.671   6.930   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+1
HETATM   70  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   74  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
CONECT    1    8   19                                                       
CONECT    2   10   19                                                       
CONECT    3    6   20                                                       
CONECT    4    7   20                                                       
CONECT    5    9   21                                                       
CONECT    6    3   22                                                       
CONECT    7    4   22                                                       
CONECT    8    1   25                                                       
CONECT    9    5   26                                                       
CONECT   10    2   35                                                       
CONECT   11   19   27                                                       
CONECT   12   21   28                                                       
CONECT   13   23   29                                                       
CONECT   14   23   30                                                       
CONECT   15   24   31                                                       
CONECT   16   32   50                                                       
CONECT   17   33   67                                                       
CONECT   18   34   68                                                       
CONECT   19    1    2   11                                                  
CONECT   20    3    4   46                                                  
CONECT   21    5   12   44                                                  
CONECT   22    6    7   51                                                  
CONECT   23   13   14   52                                                  
CONECT   24   15   29   30                                                  
CONECT   25    8   27   53                                                  
CONECT   26    9   28   54                                                  
CONECT   27   11   25   55                                                  
CONECT   28   12   26   56                                                  
CONECT   29   13   24   69                                                  
CONECT   30   14   24   70                                                  
CONECT   31   15   44   71                                                  
CONECT   32   16   36   72                                                  
CONECT   33   17   38   74                                                  
CONECT   34   18   37   73                                                  
CONECT   35   10   57   67                                                  
CONECT   36   32   39   58                                                  
CONECT   37   34   40   59                                                  
CONECT   38   33   41   60                                                  
CONECT   39   36   42   61                                                  
CONECT   40   37   43   62                                                  
CONECT   41   38   45   63                                                  
CONECT   42   39   47   64                                                  
CONECT   43   40   48   65                                                  
CONECT   44   21   31   69                                                  
CONECT   45   41   49   75                                                  
CONECT   46   20   66   68                                                  
CONECT   47   42   70   72                                                  
CONECT   48   43   73   75                                                  
CONECT   49   45   71   74                                                  
CONECT   50   16                                                            
CONECT   51   22                                                            
CONECT   52   23                                                            
CONECT   53   25                                                            
CONECT   54   26                                                            
CONECT   55   27                                                            
CONECT   56   28                                                            
CONECT   57   35                                                            
CONECT   58   36                                                            
CONECT   59   37                                                            
CONECT   60   38                                                            
CONECT   61   39                                                            
CONECT   62   40                                                            
CONECT   63   41                                                            
CONECT   64   42                                                            
CONECT   65   43                                                            
CONECT   66   46                                                            
CONECT   67   17   35                                                       
CONECT   68   18   46                                                       
CONECT   69   29   44                                                       
CONECT   70   30   47                                                       
CONECT   71   31   49                                                       
CONECT   72   32   47                                                       
CONECT   73   34   48                                                       
CONECT   74   33   49                                                       
CONECT   75   45   48                                                       
MASTER        0    0    0    0    0    0    0    0   75    0  164    0
END
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3D PDB for HMDB0035459 (YGM 1A)

COMPND    HMDB0035459
HETATM    1  O1  UNL     1      -9.761   2.305  -0.738  1.00  0.00           O  
HETATM    2  C1  UNL     1      -8.821   1.621  -1.255  1.00  0.00           C  
HETATM    3  C2  UNL     1      -9.220   0.487  -2.082  1.00  0.00           C  
HETATM    4  C3  UNL     1      -8.224  -0.242  -2.634  1.00  0.00           C  
HETATM    5  C4  UNL     1      -6.840   0.098  -2.405  1.00  0.00           C  
HETATM    6  C5  UNL     1      -5.861  -0.642  -2.950  1.00  0.00           C  
HETATM    7  O2  UNL     1      -6.255  -1.720  -3.724  1.00  0.00           O  
HETATM    8  O3  UNL     1      -4.534  -0.313  -2.726  1.00  0.00           O  
HETATM    9  C6  UNL     1      -3.540  -0.770  -3.584  1.00  0.00           C  
HETATM   10  C7  UNL     1      -2.161  -0.270  -3.098  1.00  0.00           C  
HETATM   11  O4  UNL     1      -1.973  -0.769  -1.823  1.00  0.00           O  
HETATM   12  C8  UNL     1      -0.690  -0.593  -1.343  1.00  0.00           C  
HETATM   13  O5  UNL     1      -0.649  -1.348  -0.194  1.00  0.00           O  
HETATM   14  C9  UNL     1       0.310  -2.285  -0.098  1.00  0.00           C  
HETATM   15  C10 UNL     1       0.870  -2.344   1.262  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.191  -1.082   1.844  1.00  0.00           O  
HETATM   17  C11 UNL     1       2.380  -0.428   1.869  1.00  0.00           C  
HETATM   18  C12 UNL     1       3.420  -0.945   1.094  1.00  0.00           C  
HETATM   19  C13 UNL     1       4.625  -0.275   1.130  1.00  0.00           C  
HETATM   20  C14 UNL     1       5.688  -0.778   0.360  1.00  0.00           C  
HETATM   21  O7  UNL     1       5.470  -1.919  -0.395  1.00  0.00           O  
HETATM   22  C15 UNL     1       6.474  -2.507  -1.143  1.00  0.00           C  
HETATM   23  O8  UNL     1       6.310  -2.261  -2.532  1.00  0.00           O  
HETATM   24  C16 UNL     1       7.616  -2.203  -3.077  1.00  0.00           C  
HETATM   25  C17 UNL     1       7.583  -2.034  -4.556  1.00  0.00           C  
HETATM   26  O9  UNL     1       6.928  -3.073  -5.216  1.00  0.00           O  
HETATM   27  C18 UNL     1       8.434  -3.372  -2.597  1.00  0.00           C  
HETATM   28  O10 UNL     1       9.097  -3.898  -3.721  1.00  0.00           O  
HETATM   29  C19 UNL     1       7.636  -4.475  -1.972  1.00  0.00           C  
HETATM   30  O11 UNL     1       8.540  -5.232  -1.198  1.00  0.00           O  
HETATM   31  C20 UNL     1       6.561  -4.015  -1.029  1.00  0.00           C  
HETATM   32  O12 UNL     1       6.757  -4.358   0.284  1.00  0.00           O  
HETATM   33  C21 UNL     1       6.875  -0.105   0.407  1.00  0.00           C  
HETATM   34  C22 UNL     1       7.001   1.046   1.204  1.00  0.00           C  
HETATM   35  O13 UNL     1       8.238   1.673   1.199  1.00  0.00           O  
HETATM   36  C23 UNL     1       5.943   1.503   1.939  1.00  0.00           C  
HETATM   37  C24 UNL     1       4.700   0.840   1.922  1.00  0.00           C  
HETATM   38  O14 UNL     1       3.709   1.291   2.628  1.00  0.00           O1+
HETATM   39  C25 UNL     1       2.507   0.690   2.642  1.00  0.00           C  
HETATM   40  C26 UNL     1       1.472   1.293   3.482  1.00  0.00           C  
HETATM   41  C27 UNL     1       1.727   2.548   4.060  1.00  0.00           C  
HETATM   42  C28 UNL     1       0.844   3.152   4.923  1.00  0.00           C  
HETATM   43  C29 UNL     1      -0.358   2.524   5.257  1.00  0.00           C  
HETATM   44  O15 UNL     1      -1.253   3.122   6.124  1.00  0.00           O  
HETATM   45  C30 UNL     1      -0.615   1.298   4.698  1.00  0.00           C  
HETATM   46  O16 UNL     1      -1.775   0.602   4.975  1.00  0.00           O  
HETATM   47  C31 UNL     1       0.307   0.691   3.811  1.00  0.00           C  
HETATM   48  O17 UNL     1       0.126  -3.020   2.155  1.00  0.00           O  
HETATM   49  C32 UNL     1      -1.067  -3.548   1.967  1.00  0.00           C  
HETATM   50  C33 UNL     1      -2.256  -2.874   2.593  1.00  0.00           C  
HETATM   51  O18 UNL     1      -2.407  -1.552   2.213  1.00  0.00           O  
HETATM   52  C34 UNL     1      -3.415  -0.707   2.547  1.00  0.00           C  
HETATM   53  O19 UNL     1      -4.334  -1.162   3.272  1.00  0.00           O  
HETATM   54  C35 UNL     1      -3.486   0.712   2.110  1.00  0.00           C  
HETATM   55  C36 UNL     1      -4.498   1.465   2.469  1.00  0.00           C  
HETATM   56  C37 UNL     1      -4.693   2.862   2.115  1.00  0.00           C  
HETATM   57  C38 UNL     1      -3.773   3.573   1.380  1.00  0.00           C  
HETATM   58  C39 UNL     1      -4.023   4.925   1.084  1.00  0.00           C  
HETATM   59  C40 UNL     1      -5.144   5.558   1.500  1.00  0.00           C  
HETATM   60  O20 UNL     1      -5.366   6.911   1.193  1.00  0.00           O  
HETATM   61  C41 UNL     1      -6.078   4.867   2.236  1.00  0.00           C  
HETATM   62  O21 UNL     1      -7.254   5.489   2.681  1.00  0.00           O  
HETATM   63  C42 UNL     1      -5.839   3.545   2.528  1.00  0.00           C  
HETATM   64  C43 UNL     1      -1.422  -3.941   0.552  1.00  0.00           C  
HETATM   65  O22 UNL     1      -2.471  -3.183   0.054  1.00  0.00           O  
HETATM   66  C44 UNL     1      -0.241  -3.719  -0.359  1.00  0.00           C  
HETATM   67  O23 UNL     1      -0.484  -3.938  -1.680  1.00  0.00           O  
HETATM   68  C45 UNL     1      -0.476   0.883  -1.176  1.00  0.00           C  
HETATM   69  O24 UNL     1      -0.175   1.284   0.102  1.00  0.00           O  
HETATM   70  C46 UNL     1      -1.686   1.673  -1.664  1.00  0.00           C  
HETATM   71  O25 UNL     1      -1.245   3.016  -1.695  1.00  0.00           O  
HETATM   72  C47 UNL     1      -2.171   1.237  -3.007  1.00  0.00           C  
HETATM   73  O26 UNL     1      -1.458   1.769  -4.081  1.00  0.00           O  
HETATM   74  C48 UNL     1      -6.486   1.230  -1.580  1.00  0.00           C  
HETATM   75  C49 UNL     1      -7.443   1.991  -1.005  1.00  0.00           C  
HETATM   76  H1  UNL     1     -10.253   0.234  -2.257  1.00  0.00           H  
HETATM   77  H2  UNL     1      -8.558  -1.078  -3.243  1.00  0.00           H  
HETATM   78  H3  UNL     1      -7.005  -1.760  -4.373  1.00  0.00           H  
HETATM   79  H4  UNL     1      -3.717  -0.487  -4.646  1.00  0.00           H  
HETATM   80  H5  UNL     1      -3.505  -1.877  -3.547  1.00  0.00           H  
HETATM   81  H6  UNL     1      -1.402  -0.668  -3.776  1.00  0.00           H  
HETATM   82  H7  UNL     1       0.025  -0.925  -2.117  1.00  0.00           H  
HETATM   83  H8  UNL     1       1.114  -2.180  -0.885  1.00  0.00           H  
HETATM   84  H9  UNL     1       1.913  -2.850   1.224  1.00  0.00           H  
HETATM   85  H10 UNL     1       3.346  -1.814   0.475  1.00  0.00           H  
HETATM   86  H11 UNL     1       7.484  -2.132  -0.873  1.00  0.00           H  
HETATM   87  H12 UNL     1       8.054  -1.281  -2.628  1.00  0.00           H  
HETATM   88  H13 UNL     1       8.593  -1.904  -4.983  1.00  0.00           H  
HETATM   89  H14 UNL     1       7.044  -1.078  -4.774  1.00  0.00           H  
HETATM   90  H15 UNL     1       6.951  -2.805  -6.192  1.00  0.00           H  
HETATM   91  H16 UNL     1       9.216  -3.060  -1.880  1.00  0.00           H  
HETATM   92  H17 UNL     1       9.870  -3.332  -3.974  1.00  0.00           H  
HETATM   93  H18 UNL     1       7.238  -5.198  -2.728  1.00  0.00           H  
HETATM   94  H19 UNL     1       8.897  -4.713  -0.430  1.00  0.00           H  
HETATM   95  H20 UNL     1       5.592  -4.506  -1.353  1.00  0.00           H  
HETATM   96  H21 UNL     1       7.142  -5.266   0.397  1.00  0.00           H  
HETATM   97  H22 UNL     1       7.736  -0.416  -0.153  1.00  0.00           H  
HETATM   98  H23 UNL     1       9.023   1.357   0.679  1.00  0.00           H  
HETATM   99  H24 UNL     1       6.040   2.397   2.553  1.00  0.00           H  
HETATM  100  H25 UNL     1       2.668   3.023   3.780  1.00  0.00           H  
HETATM  101  H26 UNL     1       1.060   4.133   5.372  1.00  0.00           H  
HETATM  102  H27 UNL     1      -2.128   2.749   6.433  1.00  0.00           H  
HETATM  103  H28 UNL     1      -2.486   0.943   5.591  1.00  0.00           H  
HETATM  104  H29 UNL     1       0.057  -0.273   3.402  1.00  0.00           H  
HETATM  105  H30 UNL     1      -1.034  -4.561   2.521  1.00  0.00           H  
HETATM  106  H31 UNL     1      -2.172  -2.863   3.727  1.00  0.00           H  
HETATM  107  H32 UNL     1      -3.192  -3.484   2.435  1.00  0.00           H  
HETATM  108  H33 UNL     1      -2.712   1.157   1.496  1.00  0.00           H  
HETATM  109  H34 UNL     1      -5.252   0.982   3.087  1.00  0.00           H  
HETATM  110  H35 UNL     1      -2.873   3.132   1.027  1.00  0.00           H  
HETATM  111  H36 UNL     1      -3.291   5.473   0.507  1.00  0.00           H  
HETATM  112  H37 UNL     1      -6.210   7.366   1.519  1.00  0.00           H  
HETATM  113  H38 UNL     1      -7.901   4.926   3.221  1.00  0.00           H  
HETATM  114  H39 UNL     1      -6.545   2.964   3.101  1.00  0.00           H  
HETATM  115  H40 UNL     1      -1.725  -4.997   0.476  1.00  0.00           H  
HETATM  116  H41 UNL     1      -2.991  -3.739  -0.573  1.00  0.00           H  
HETATM  117  H42 UNL     1       0.590  -4.371  -0.037  1.00  0.00           H  
HETATM  118  H43 UNL     1      -1.368  -3.531  -1.934  1.00  0.00           H  
HETATM  119  H44 UNL     1       0.372   1.245  -1.840  1.00  0.00           H  
HETATM  120  H45 UNL     1       0.594   1.907   0.139  1.00  0.00           H  
HETATM  121  H46 UNL     1      -2.484   1.617  -0.902  1.00  0.00           H  
HETATM  122  H47 UNL     1      -1.553   3.532  -0.916  1.00  0.00           H  
HETATM  123  H48 UNL     1      -3.257   1.547  -3.101  1.00  0.00           H  
HETATM  124  H49 UNL     1      -2.058   2.247  -4.703  1.00  0.00           H  
HETATM  125  H50 UNL     1      -5.468   1.514  -1.383  1.00  0.00           H  
HETATM  126  H51 UNL     1      -7.210   2.836  -0.389  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   75
CONECT    3    4    4   76
CONECT    4    5   77
CONECT    5    6    6   74
CONECT    6    7    8
CONECT    7   78
CONECT    8    9
CONECT    9   10   79   80
CONECT   10   11   72   81
CONECT   11   12
CONECT   12   13   68   82
CONECT   13   14
CONECT   14   15   66   83
CONECT   15   16   48   84
CONECT   16   17
CONECT   17   18   18   39
CONECT   18   19   85
CONECT   19   20   20   37
CONECT   20   21   33
CONECT   21   22
CONECT   22   23   31   86
CONECT   23   24
CONECT   24   25   27   87
CONECT   25   26   88   89
CONECT   26   90
CONECT   27   28   29   91
CONECT   28   92
CONECT   29   30   31   93
CONECT   30   94
CONECT   31   32   95
CONECT   32   96
CONECT   33   34   34   97
CONECT   34   35   36
CONECT   35   98
CONECT   36   37   37   99
CONECT   37   38
CONECT   38   39   39
CONECT   39   40
CONECT   40   41   41   47
CONECT   41   42  100
CONECT   42   43   43  101
CONECT   43   44   45
CONECT   44  102
CONECT   45   46   47   47
CONECT   46  103
CONECT   47  104
CONECT   48   49
CONECT   49   50   64  105
CONECT   50   51  106  107
CONECT   51   52
CONECT   52   53   53   54
CONECT   54   55   55  108
CONECT   55   56  109
CONECT   56   57   57   63
CONECT   57   58  110
CONECT   58   59   59  111
CONECT   59   60   61
CONECT   60  112
CONECT   61   62   63   63
CONECT   62  113
CONECT   63  114
CONECT   64   65   66  115
CONECT   65  116
CONECT   66   67  117
CONECT   67  118
CONECT   68   69   70  119
CONECT   69  120
CONECT   70   71   72  121
CONECT   71  122
CONECT   72   73  123
CONECT   73  124
CONECT   74   75   75  125
CONECT   75  126
END
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SMILES for HMDB0035459 (YGM 1A)

OCC1OC(OC2=CC(O)=CC3=[O+]C(=C(OC4OC(COC(=O)\C=C\C5=CC(O)=C(O)C=C5)C(O)C(O)C4OC4OC(COC(O)=C5C=CC(=O)C=C5)C(O)C(O)C4O)C=C23)C2=CC(O)=C(O)C=C2)C(O)C(O)C1O
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INCHI for HMDB0035459 (YGM 1A)

InChI=1S/C49H50O26/c50-16-32-36(58)39(61)42(64)47(72-32)70-30-14-23(52)13-29-24(30)15-31(44(69-29)21-5-9-26(54)28(56)12-21)71-49-45(41(63)38(60)33(74-49)17-67-35(57)10-2-19-1-8-25(53)27(55)11-19)75-48-43(65)40(62)37(59)34(73-48)18-68-46(66)20-3-6-22(51)7-4-20/h1-15,32-34,36-43,45,47-50,58-65H,16-18H2,(H5-,51,52,53,54,55,56,57,66)/p+1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC49H51O26
Average Molecular Weight1055.9136
Monoisotopic Molecular Weight1055.266856804
IUPAC Name2-(3,4-dihydroxyphenyl)-3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-[(3,4,5-trihydroxy-6-{[hydroxy(4-oxocyclohexa-2,5-dien-1-ylidene)methoxy]methyl}oxan-2-yl)oxy]oxan-2-yl]oxy}-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
Traditional Name2-(3,4-dihydroxyphenyl)-3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-[(3,4,5-trihydroxy-6-{[hydroxy(4-oxocyclohexa-2,5-dien-1-ylidene)methoxy]methyl}oxan-2-yl)oxy]oxan-2-yl]oxy}-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
OCC1OC(OC2=CC(O)=CC3=[O+]C(=C(OC4OC(COC(=O)\C=C\C5=CC(O)=C(O)C=C5)C(O)C(O)C4OC4OC(COC(O)=C5C=CC(=O)C=C5)C(O)C(O)C4O)C=C23)C2=CC(O)=C(O)C=C2)C(O)C(O)C1O
InChI Identifier
InChI=1S/C49H50O26/c50-16-32-36(58)39(61)42(64)47(72-32)70-30-14-23(52)13-29-24(30)15-31(44(69-29)21-5-9-26(54)28(56)12-21)71-49-45(41(63)38(60)33(74-49)17-67-35(57)10-2-19-1-8-25(53)27(55)11-19)75-48-43(65)40(62)37(59)34(73-48)18-68-46(66)20-3-6-22(51)7-4-20/h1-15,32-34,36-43,45,47-50,58-65H,16-18H2,(H5-,51,52,53,54,55,56,57,66)/p+1
InChI KeyGLMCQQPCNPVXHL-UHFFFAOYSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as anthocyanidin 3-o-6-p-coumaroyl glycosides. These are anthocyanidin 3-O-glycosides where the carbohydrate moiety is esterified at the C6 position with a p-coumaric acid. P-coumaric acid is an organic derivative of cinnamic acid, that carries a hydroxyl group at the 4-position of the benzene ring.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassFlavonoids
Sub ClassFlavonoid glycosides
Direct ParentAnthocyanidin 3-O-6-p-coumaroyl glycosides
Alternative Parents
Substituents
  • Anthocyanidin 3-o-6-p-coumaroyl-glycoside
  • Anthocyanidin-3-o-glycoside
  • Anthocyanidin-5-o-glycoside
  • Anthocyanin
  • Flavonoid-3-o-glycoside
  • 3'-hydroxyflavonoid
  • 4'-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Hydroxyflavonoid
  • Anthocyanidin
  • Phenolic glycoside
  • Cinnamic acid or derivatives
  • Coumaric acid or derivatives
  • Hydroxycinnamic acid or derivatives
  • Cinnamic acid ester
  • Disaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • 1-benzopyran
  • Benzopyran
  • Styrene
  • Quinomethane
  • Catechol
  • P-quinomethane
  • Phenol
  • 1-hydroxy-4-unsubstituted benzenoid
  • Fatty acid ester
  • 1-hydroxy-2-unsubstituted benzenoid
  • Fatty acyl
  • Monocyclic benzene moiety
  • Benzenoid
  • Oxane
  • Alpha,beta-unsaturated carboxylic ester
  • Enoate ester
  • Heteroaromatic compound
  • Ketone
  • Secondary alcohol
  • Carboxylic acid ester
  • Ketene acetal or derivatives
  • Cyclic ketone
  • Monocarboxylic acid or derivatives
  • Acetal
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid derivative
  • Oxacycle
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Primary alcohol
  • Carbonyl group
  • 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
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.24 g/LALOGPS
logP1.69ALOGPS
logP0.61ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)6.17ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count24ChemAxon
Hydrogen Donor Count15ChemAxon
Polar Surface Area424.57 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity268.85 m³·mol⁻¹ChemAxon
Polarizability101.93 ųChemAxon
Number of Rings8ChemAxon
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]-348.05830932474
DeepCCS[M+Na]+322.07430932474
AllCCS[M+H]+292.732859911
AllCCS[M+H-H2O]+293.532859911
AllCCS[M+NH4]+291.932859911
AllCCS[M+Na]+291.632859911
AllCCS[M-H]-270.432859911
AllCCS[M+Na-2H]-275.732859911
AllCCS[M+HCOO]-281.632859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.3.22 minutes32390414
Predicted by Siyang on May 30, 202213.9928 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.85 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid362.3 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1908.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid207.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid140.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid203.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid114.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid433.9 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid473.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)1118.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid931.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid470.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1328.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid305.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid320.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate459.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA622.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water238.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
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 IDFDB014144
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131751768
PDB IDNot Available
ChEBI ID178043
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.. .

Enzymes

Enzyme Details
1. Liver carboxylesterase 1
General function:
Lipid transport and metabolism
Specific function:
Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Hydrolyzes aromatic and aliphatic esters, but has no catalytic activity toward amides or a fatty acyl-CoA ester. Hydrolyzes the methyl ester group of cocaine to form benzoylecgonine. Catalyzes the transesterification of cocaine to form cocaethylene. Displays fatty acid ethyl ester synthase activity, catalyzing the ethyl esterification of oleic acid to ethyloleate.
Gene Name:
CES1
Uniprot ID:
P23141
Molecular weight:
62520.62
Reactions
YGM 1A → 3-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-{[hydroxy(4-oxocyclohexa-2,5-dien-1-ylidene)methoxy]methyl}oxan-2-yl)oxy]oxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-yliumdetails