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Showing metabocard for Pelargonidin 3-(6''-malonylglucoside) (HMDB0303647)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 03:32:25 UTC
Update Date2021-09-24 03:32:25 UTC
HMDB IDHMDB0303647
Secondary Accession NumbersNone
Metabolite Identification
Common NamePelargonidin 3-(6''-malonylglucoside)
DescriptionPelargonidin 3-(6''-malonylglucoside) is a member of the class of compounds known as anthocyanidin-3-o-glycosides. Anthocyanidin-3-o-glycosides are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position. Pelargonidin 3-(6''-malonylglucoside) is practically insoluble (in water) and a weakly acidic compound (based on its pKa). Pelargonidin 3-(6''-malonylglucoside) can be found in cloudberry, lupine, red raspberry, and strawberry, which makes pelargonidin 3-(6''-malonylglucoside) a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

Pelargonidin 3-O-(6''-malonyl-glucoside)
  Mrv1652309231720592D          

 37 40  0  0  1  0            999 V2000
    0.0000   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -4.9499    0.0000 C   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
    1.4289   -4.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   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   -4.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5724   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0012   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  2 36  1  0  0  0  0
 36 37  1  6  0  0  0
M  CHG  1  25   1
M  END
Download

3D MOL for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

HMDB0303647
     RDKit          3D
Pelargonidin 3-(6''-malonylglucoside)
 60 63  0  0  0  0  0  0  0  0999 V2000
    6.4098    3.0358   -0.9300 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2625    2.1209   -1.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6035    2.3823   -0.9250 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7868    0.7576   -1.3564 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2917    0.7181   -1.4561 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6194    1.7435   -1.2970 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6754   -0.4709   -1.7263 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2891   -0.6830   -1.8506 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5888   -0.3318   -0.5422 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2176   -0.5569   -0.6879 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5268   -0.2915    0.4966 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -3.8891    4.4927    1.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1185    3.9413    0.8052 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7603   -2.0382   -0.6315 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3713    0.6212    1.3884 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
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 32 33  1  0
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 36  9  1  0
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 31 25  1  0
 22 15  1  0
  3 38  1  0
  4 39  1  0
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 32 55  1  1
 33 56  1  0
 34 57  1  1
 35 58  1  0
 36 59  1  6
 37 60  1  0
M  CHG  1  23   1
M  END
Download

3D SDF for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

Pelargonidin 3-O-(6''-malonyl-glucoside)
  Mrv1652309231720592D          

 37 40  0  0  1  0            999 V2000
    0.0000   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -4.9499    0.0000 C   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
    1.4289   -4.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   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   -4.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5724   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0012   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8579   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  1  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
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
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  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  3 12  1  0  0  0  0
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 18 20  1  0  0  0  0
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 23 24  2  0  0  0  0
 17 24  1  0  0  0  0
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 25 26  2  0  0  0  0
 15 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 27 33  1  0  0  0  0
 13 34  1  0  0  0  0
 34 35  1  1  0  0  0
 34 36  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  1  6  0  0  0
M  CHG  1  25   1
M  END
> <DATABASE_ID>
HMDB0303647

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@@H]1[C@@H](COC(=O)CC(O)=O)O[C@@H](OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H22O13/c25-11-3-1-10(2-4-11)23-16(7-13-14(27)5-12(26)6-15(13)35-23)36-24-22(33)21(32)20(31)17(37-24)9-34-19(30)8-18(28)29/h1-7,17,20-22,24,31-33H,8-9H2,(H3-,25,26,27,28,29)/p+1/t17-,20-,21+,22-,24-/m1/s1

> <INCHI_KEY>
XLZUBCUKXQFBKB-JZWLZXDTSA-O

> <FORMULA>
C24H23O13

> <MOLECULAR_WEIGHT>
519.4316

> <EXACT_MASS>
519.113865822

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
48.88325338945592

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
1.90

> <JCHEM_LOGP>
0.9598999999999989

> <ALOGPS_LOGS>
-3.25

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.397137470862175

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2955237885215536

> <JCHEM_PKA_STRONGEST_BASIC>
-3.64910309071837

> <JCHEM_POLAR_SURFACE_AREA>
216.57999999999998

> <JCHEM_REFRACTIVITY>
129.77219999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.14e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

HMDB0303647
     RDKit          3D
Pelargonidin 3-(6''-malonylglucoside)
 60 63  0  0  0  0  0  0  0  0999 V2000
    6.4098    3.0358   -0.9300 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2625    2.1209   -1.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6035    2.3823   -0.9250 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7868    0.7576   -1.3564 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2917    0.7181   -1.4561 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6194    1.7435   -1.2970 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6754   -0.4709   -1.7263 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2891   -0.6830   -1.8506 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5888   -0.3318   -0.5422 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2176   -0.5569   -0.6879 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5268   -0.2915    0.4966 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8132   -0.5532    0.2546 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9218    0.2078    0.2980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7616    1.5506    0.6524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8730    2.3564    0.7065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7660    3.6959    1.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4997    4.1838    1.3406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8891    4.4927    1.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1185    3.9413    0.8052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2692    4.7477    0.8543 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2007    2.6190    0.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0812    1.7865    0.4064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1946    0.5365    0.0811 O   0  0  0  0  0  3  0  0  0  0  0  0
   -3.1594   -0.3037    0.0084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4347   -1.6747   -0.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4770   -2.6359   -0.4818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8025   -3.9487   -0.8504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1158   -4.2542   -1.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4639   -5.5471   -1.4643 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1090   -3.3115   -0.9933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7603   -2.0382   -0.6315 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9574   -1.2511    1.6014 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5180   -0.4923    2.6217 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0532   -2.1210    1.0250 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6227   -2.8148   -0.1042 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1454   -1.1595    0.5668 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4444   -0.3244    1.6413 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.1550    2.0727   -0.1331 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1649    0.4016   -2.3364 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0692    0.0299   -0.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0738   -1.7237   -2.1485 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8960   -0.0270   -2.6808 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7915    0.7384   -0.3295 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6918    0.7485    0.7784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8184    1.9812    0.8832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3438    5.1500    1.6009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8157    5.5448    1.3745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5143    5.2237   -0.0244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1802    2.1791    0.2282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4243   -2.4580   -0.3002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0129   -4.6845   -0.9302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7074   -6.2500   -0.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1564   -3.5719   -1.1948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5569   -1.2812   -0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1312   -1.8214    2.0233 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5864   -1.0604    3.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4379   -2.8586    1.7556 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -3.3330    0.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0499   -1.7333    0.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3713    0.6212    1.3884 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 28 30  1  0
 30 31  2  0
 11 32  1  0
 32 33  1  0
 32 34  1  0
 34 35  1  0
 34 36  1  0
 36 37  1  0
 36  9  1  0
 24 13  1  0
 31 25  1  0
 22 15  1  0
  3 38  1  0
  4 39  1  0
  4 40  1  0
  8 41  1  0
  8 42  1  0
  9 43  1  1
 11 44  1  1
 14 45  1  0
 17 46  1  0
 18 47  1  0
 20 48  1  0
 21 49  1  0
 26 50  1  0
 27 51  1  0
 29 52  1  0
 30 53  1  0
 31 54  1  0
 32 55  1  1
 33 56  1  0
 34 57  1  1
 35 58  1  0
 36 59  1  6
 37 60  1  0
M  CHG  1  23   1
M  END
Download

PDB for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

HEADER    PROTEIN                                 23-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Pelargonidin 3-O-(6''-malonyl-glucoside)          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-SEP-17         0                                  
HETATM    1  O   UNK     0       0.000 -12.320   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668 -10.010   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -6.668 -14.630   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -9.336 -14.630   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0     -12.003 -14.630   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0     -10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -9.336 -10.010   0.000  0.00  0.00           O+1
HETATM   26  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -5.335 -12.320   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -2.667 -13.860   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   36                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    3   13                                                       
CONECT   13   12   14   34                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   26                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   24                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   17   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   15   27                                                  
CONECT   27   26   28   33                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   27                                                       
CONECT   34   13   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34    2   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END
Download

3D PDB for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

COMPND    HMDB0303647
HETATM    1  O1  UNL     1       6.410   3.036  -0.930  1.00  0.00           O  
HETATM    2  C1  UNL     1       7.262   2.121  -1.058  1.00  0.00           C  
HETATM    3  O2  UNL     1       8.604   2.382  -0.925  1.00  0.00           O  
HETATM    4  C2  UNL     1       6.787   0.758  -1.356  1.00  0.00           C  
HETATM    5  C3  UNL     1       5.292   0.718  -1.456  1.00  0.00           C  
HETATM    6  O3  UNL     1       4.619   1.744  -1.297  1.00  0.00           O  
HETATM    7  O4  UNL     1       4.675  -0.471  -1.726  1.00  0.00           O  
HETATM    8  C4  UNL     1       3.289  -0.683  -1.851  1.00  0.00           C  
HETATM    9  C5  UNL     1       2.589  -0.332  -0.542  1.00  0.00           C  
HETATM   10  O5  UNL     1       1.218  -0.557  -0.688  1.00  0.00           O  
HETATM   11  C6  UNL     1       0.527  -0.292   0.497  1.00  0.00           C  
HETATM   12  O6  UNL     1      -0.813  -0.553   0.255  1.00  0.00           O  
HETATM   13  C7  UNL     1      -1.922   0.208   0.298  1.00  0.00           C  
HETATM   14  C8  UNL     1      -1.762   1.551   0.652  1.00  0.00           C  
HETATM   15  C9  UNL     1      -2.873   2.356   0.707  1.00  0.00           C  
HETATM   16  C10 UNL     1      -2.766   3.696   1.053  1.00  0.00           C  
HETATM   17  O7  UNL     1      -1.500   4.184   1.341  1.00  0.00           O  
HETATM   18  C11 UNL     1      -3.889   4.493   1.104  1.00  0.00           C  
HETATM   19  C12 UNL     1      -5.119   3.941   0.805  1.00  0.00           C  
HETATM   20  O8  UNL     1      -6.269   4.748   0.854  1.00  0.00           O  
HETATM   21  C13 UNL     1      -5.201   2.619   0.466  1.00  0.00           C  
HETATM   22  C14 UNL     1      -4.081   1.787   0.406  1.00  0.00           C  
HETATM   23  O9  UNL     1      -4.195   0.537   0.081  1.00  0.00           O1+
HETATM   24  C15 UNL     1      -3.159  -0.304   0.008  1.00  0.00           C  
HETATM   25  C16 UNL     1      -3.435  -1.675  -0.368  1.00  0.00           C  
HETATM   26  C17 UNL     1      -2.477  -2.636  -0.482  1.00  0.00           C  
HETATM   27  C18 UNL     1      -2.802  -3.949  -0.850  1.00  0.00           C  
HETATM   28  C19 UNL     1      -4.116  -4.254  -1.098  1.00  0.00           C  
HETATM   29  O10 UNL     1      -4.464  -5.547  -1.464  1.00  0.00           O  
HETATM   30  C20 UNL     1      -5.109  -3.311  -0.993  1.00  0.00           C  
HETATM   31  C21 UNL     1      -4.760  -2.038  -0.632  1.00  0.00           C  
HETATM   32  C22 UNL     1       0.957  -1.251   1.601  1.00  0.00           C  
HETATM   33  O11 UNL     1       1.518  -0.492   2.622  1.00  0.00           O  
HETATM   34  C23 UNL     1       2.053  -2.121   1.025  1.00  0.00           C  
HETATM   35  O12 UNL     1       1.623  -2.815  -0.104  1.00  0.00           O  
HETATM   36  C24 UNL     1       3.145  -1.160   0.567  1.00  0.00           C  
HETATM   37  O13 UNL     1       3.444  -0.324   1.641  1.00  0.00           O  
HETATM   38  H1  UNL     1       9.155   2.073  -0.133  1.00  0.00           H  
HETATM   39  H2  UNL     1       7.165   0.402  -2.336  1.00  0.00           H  
HETATM   40  H3  UNL     1       7.069   0.030  -0.570  1.00  0.00           H  
HETATM   41  H4  UNL     1       3.074  -1.724  -2.148  1.00  0.00           H  
HETATM   42  H5  UNL     1       2.896  -0.027  -2.681  1.00  0.00           H  
HETATM   43  H6  UNL     1       2.791   0.738  -0.330  1.00  0.00           H  
HETATM   44  H7  UNL     1       0.692   0.748   0.778  1.00  0.00           H  
HETATM   45  H8  UNL     1      -0.818   1.981   0.883  1.00  0.00           H  
HETATM   46  H9  UNL     1      -1.344   5.150   1.601  1.00  0.00           H  
HETATM   47  H10 UNL     1      -3.816   5.545   1.374  1.00  0.00           H  
HETATM   48  H11 UNL     1      -6.514   5.224  -0.024  1.00  0.00           H  
HETATM   49  H12 UNL     1      -6.180   2.179   0.228  1.00  0.00           H  
HETATM   50  H13 UNL     1      -1.424  -2.458  -0.300  1.00  0.00           H  
HETATM   51  H14 UNL     1      -2.013  -4.684  -0.930  1.00  0.00           H  
HETATM   52  H15 UNL     1      -4.707  -6.250  -0.753  1.00  0.00           H  
HETATM   53  H16 UNL     1      -6.156  -3.572  -1.195  1.00  0.00           H  
HETATM   54  H17 UNL     1      -5.557  -1.281  -0.547  1.00  0.00           H  
HETATM   55  H18 UNL     1       0.131  -1.821   2.023  1.00  0.00           H  
HETATM   56  H19 UNL     1       1.586  -1.060   3.434  1.00  0.00           H  
HETATM   57  H20 UNL     1       2.438  -2.859   1.756  1.00  0.00           H  
HETATM   58  H21 UNL     1       0.810  -3.333   0.042  1.00  0.00           H  
HETATM   59  H22 UNL     1       4.050  -1.733   0.279  1.00  0.00           H  
HETATM   60  H23 UNL     1       3.371   0.621   1.388  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   38
CONECT    4    5   39   40
CONECT    5    6    6    7
CONECT    7    8
CONECT    8    9   41   42
CONECT    9   10   36   43
CONECT   10   11
CONECT   11   12   32   44
CONECT   12   13
CONECT   13   14   14   24
CONECT   14   15   45
CONECT   15   16   16   22
CONECT   16   17   18
CONECT   17   46
CONECT   18   19   19   47
CONECT   19   20   21
CONECT   20   48
CONECT   21   22   22   49
CONECT   22   23
CONECT   23   24   24
CONECT   24   25
CONECT   25   26   26   31
CONECT   26   27   50
CONECT   27   28   28   51
CONECT   28   29   30
CONECT   29   52
CONECT   30   31   31   53
CONECT   31   54
CONECT   32   33   34   55
CONECT   33   56
CONECT   34   35   36   57
CONECT   35   58
CONECT   36   37   59
CONECT   37   60
END
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SMILES for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

O[C@@H]1[C@@H](COC(=O)CC(O)=O)O[C@@H](OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@H](O)[C@H]1O
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INCHI for HMDB0303647 (Pelargonidin 3-(6''-malonylglucoside))

InChI=1S/C24H22O13/c25-11-3-1-10(2-4-11)23-16(7-13-14(27)5-12(26)6-15(13)35-23)36-24-22(33)21(32)20(31)17(37-24)9-34-19(30)8-18(28)29/h1-7,17,20-22,24,31-33H,8-9H2,(H3-,25,26,27,28,29)/p+1/t17-,20-,21+,22-,24-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Pelargonidin 3-O-(6-O-malonyl-b-D-glucoside)Generator
Pelargonidin 3-O-(6-O-malonyl-β-D-glucoside)Generator
Chemical FormulaC24H23O13
Average Molecular Weight519.4316
Monoisotopic Molecular Weight519.113865822
IUPAC Name3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium
Traditional Name3-{[(2S,3R,4S,5S,6R)-6-{[(2-carboxyacetyl)oxy]methyl}-3,4,5-trihydroxyoxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
O[C@@H]1[C@@H](COC(=O)CC(O)=O)O[C@@H](OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C24H22O13/c25-11-3-1-10(2-4-11)23-16(7-13-14(27)5-12(26)6-15(13)35-23)36-24-22(33)21(32)20(31)17(37-24)9-34-19(30)8-18(28)29/h1-7,17,20-22,24,31-33H,8-9H2,(H3-,25,26,27,28,29)/p+1/t17-,20-,21+,22-,24-/m1/s1
InChI KeyXLZUBCUKXQFBKB-JZWLZXDTSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassFlavonoids
Sub ClassFlavonoid glycosides
Direct ParentAnthocyanidin-3-O-glycosides
Alternative Parents
Substituents
  • Anthocyanidin-3-o-glycoside
  • Flavonoid-3-o-glycoside
  • 4'-hydroxyflavonoid
  • 5-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Hydroxyflavonoid
  • Anthocyanidin
  • Glycosyl compound
  • O-glycosyl compound
  • Benzopyran
  • 1-benzopyran
  • 1-hydroxy-2-unsubstituted benzenoid
  • 1-hydroxy-4-unsubstituted benzenoid
  • Phenol
  • Monocyclic benzene moiety
  • 1,3-dicarbonyl compound
  • Dicarboxylic acid or derivatives
  • Monosaccharide
  • Benzenoid
  • Oxane
  • Heteroaromatic compound
  • Carboxylic acid ester
  • Secondary alcohol
  • Oxacycle
  • Acetal
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Carboxylic acid
  • Polyol
  • Organooxygen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
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
logP1.9ALOGPS
logP0.96ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)3.3ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area216.58 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity129.77 m³·mol⁻¹ChemAxon
Polarizability48.88 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
AllCCS[M+H]+215.44932859911
AllCCS[M+H-H2O]+213.62832859911
AllCCS[M+Na]+217.5832859911
AllCCS[M+NH4]+217.10932859911
AllCCS[M-H]-212.93532859911
AllCCS[M+Na-2H]-213.9932859911
AllCCS[M+HCOO]-215.30232859911
DeepCCS[M+H]+210.11930932474
DeepCCS[M-H]-207.77730932474
DeepCCS[M-2H]-241.22230932474
DeepCCS[M+Na]+215.90630932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-(6''-malonylglucoside) 10V, Positive-QTOFsplash10-00di-0000090000-cb1a1b98c6c9e5c979142016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-(6''-malonylglucoside) 20V, Positive-QTOFsplash10-00di-0000290000-f4973fa1969c99f8a9092016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-(6''-malonylglucoside) 40V, Positive-QTOFsplash10-0gxw-7930020000-5c614c6c09dbf076ba112016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-(6''-malonylglucoside) 10V, Negative-QTOFsplash10-014i-1000090000-1c8d9cf6a3f493a722152016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-(6''-malonylglucoside) 20V, Negative-QTOFsplash10-066r-9100160000-f5dba1ee5c7b0ae723ed2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-(6''-malonylglucoside) 40V, Negative-QTOFsplash10-0pb9-9600000000-dc27c6e2da063fe4f3fa2016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB017299
KNApSAcK IDC00006755
Chemspider ID391979
KEGG Compound IDC12642
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound443913
PDB IDNot Available
ChEBI ID31965
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 ReferencesNot Available