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Showing metabocard for 2-phospho-D-glycerate (HMDB0304085)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:03:01 UTC
Update Date2021-09-24 07:03:01 UTC
HMDB IDHMDB0304085
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-phospho-D-glycerate
Description2-phospho-d-glycerate, also known as 2-phosphonatoglyceric acid(3-), belongs to sugar acids and derivatives class of compounds. Those are compounds containing a saccharide unit which bears a carboxylic acid group. 2-phospho-d-glycerate is soluble (in water) and an extremely strong acidic compound (based on its pKa). 2-phospho-d-glycerate can be found in a number of food items such as wasabi, sea-buckthornberry, black chokeberry, and sweet potato, which makes 2-phospho-d-glycerate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304085 (2-phospho-D-glycerate)


  Mrv1533005141521382D          

 11 10  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.2539    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6039    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  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
  6  9  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  CHG  3   3  -1   8  -1   9  -1
M  END
Download

3D MOL for HMDB0304085 (2-phospho-D-glycerate)

HMDB0304085
     RDKit          3D
2-phospho-D-glycerate
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.6037    2.4798   -0.7115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6360    1.7343    0.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1213    2.3067    1.4743 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.1839    0.3398    0.2425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3199   -0.6583    0.3093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1584   -0.6079   -0.7769 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5761    0.0925   -0.8770 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1318   -0.4289   -0.5253 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.3894   -1.7912   -1.1692 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2037    0.7231   -1.1764 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.3944   -0.6188    1.1256 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.4638    0.1183    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9347   -0.4639    1.2212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8309   -1.6638    0.4457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3704   -1.5616   -1.0247 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  1  0
  4  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
M  CHG  3   3  -1  10  -1  11  -1
M  END
Download

3D SDF for HMDB0304085 (2-phospho-D-glycerate)


  Mrv1533005141521382D          

 11 10  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.2539    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6039    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  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
  6  9  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  CHG  3   3  -1   8  -1   9  -1
M  END
> <DATABASE_ID>
HMDB0304085

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(OP([O-])([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H7O7P/c4-1-2(3(5)6)10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/p-3

> <INCHI_KEY>
GXIURPTVHJPJLF-UHFFFAOYSA-K

> <FORMULA>
C3H4O7P

> <MOLECULAR_WEIGHT>
183.033

> <EXACT_MASS>
182.971110207

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.40177003831047

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-2-(phosphonatooxy)propanoate

> <ALOGPS_LOGP>
-1.58

> <JCHEM_LOGP>
-1.642305516

> <ALOGPS_LOGS>
-0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.483549412336351

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8080623457428864

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0640832510433764

> <JCHEM_POLAR_SURFACE_AREA>
132.78

> <JCHEM_REFRACTIVITY>
39.850100000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.00e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-2-(phosphonatooxy)propanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304085 (2-phospho-D-glycerate)

HMDB0304085
     RDKit          3D
2-phospho-D-glycerate
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.6037    2.4798   -0.7115 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6360    1.7343    0.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1213    2.3067    1.4743 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.1839    0.3398    0.2425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3199   -0.6583    0.3093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1584   -0.6079   -0.7769 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5761    0.0925   -0.8770 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1318   -0.4289   -0.5253 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.3894   -1.7912   -1.1692 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2037    0.7231   -1.1764 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.3944   -0.6188    1.1256 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.4638    0.1183    1.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9347   -0.4639    1.2212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8309   -1.6638    0.4457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3704   -1.5616   -1.0247 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  1  0
  4  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
M  CHG  3   3  -1  10  -1  11  -1
M  END
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PDB for HMDB0304085 (2-phospho-D-glycerate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       4.620   2.667   0.000  0.00  0.00           O-1
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0      -0.000   2.667   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0      -1.540   2.667   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.000   4.207   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0       0.000   1.127   0.000  0.00  0.00           O-1
HETATM   10  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    4   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0304085 (2-phospho-D-glycerate)

COMPND    HMDB0304085
HETATM    1  O1  UNL     1      -0.604   2.480  -0.712  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.636   1.734   0.303  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.121   2.307   1.474  1.00  0.00           O1-
HETATM    4  C2  UNL     1      -0.184   0.340   0.242  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.320  -0.658   0.309  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.158  -0.608  -0.777  1.00  0.00           O  
HETATM    7  O4  UNL     1       0.576   0.093  -0.877  1.00  0.00           O  
HETATM    8  P1  UNL     1       2.132  -0.429  -0.525  1.00  0.00           P  
HETATM    9  O5  UNL     1       2.389  -1.791  -1.169  1.00  0.00           O  
HETATM   10  O6  UNL     1       3.204   0.723  -1.176  1.00  0.00           O1-
HETATM   11  O7  UNL     1       2.394  -0.619   1.126  1.00  0.00           O1-
HETATM   12  H1  UNL     1       0.464   0.118   1.139  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.935  -0.464   1.221  1.00  0.00           H  
HETATM   14  H3  UNL     1      -0.831  -1.664   0.446  1.00  0.00           H  
HETATM   15  H4  UNL     1      -2.370  -1.562  -1.025  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    7   12
CONECT    5    6   13   14
CONECT    6   15
CONECT    7    8
CONECT    8    9    9   10   11
END
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SMILES for HMDB0304085 (2-phospho-D-glycerate)

OCC(OP([O-])([O-])=O)C([O-])=O
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INCHI for HMDB0304085 (2-phospho-D-glycerate)

InChI=1S/C3H7O7P/c4-1-2(3(5)6)10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/p-3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Phosphonatoglycerate(3-)ChEBI
2-Phosphonatoglyceric acid(3-)Generator
2-Phosphoglyceric acid(3-)Generator
2-Phospho-D-glyceric acidGenerator
Chemical FormulaC3H4O7P
Average Molecular Weight183.033
Monoisotopic Molecular Weight182.971110207
IUPAC Name3-hydroxy-2-(phosphonatooxy)propanoate
Traditional Name3-hydroxy-2-(phosphonatooxy)propanoate
CAS Registry NumberNot Available
SMILES
OCC(OP([O-])([O-])=O)C([O-])=O
InChI Identifier
InChI=1S/C3H7O7P/c4-1-2(3(5)6)10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/p-3
InChI KeyGXIURPTVHJPJLF-UHFFFAOYSA-K
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Glyceric_acid
  • Hydroxy acid
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
logP-1.6ALOGPS
logP-1.6ChemAxon
logS-0.53ALOGPS
pKa (Strongest Acidic)0.81ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area132.78 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity39.85 m³·mol⁻¹ChemAxon
Polarizability12.4 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+138.56432859911
AllCCS[M+H-H2O]+134.61832859911
AllCCS[M+Na]+143.29532859911
AllCCS[M+NH4]+142.23732859911
AllCCS[M-H]-117.45632859911
AllCCS[M+Na-2H]-118.94132859911
AllCCS[M+HCOO]-120.61732859911
DeepCCS[M+H]+117.7430932474
DeepCCS[M-H]-113.90730932474
DeepCCS[M-2H]-150.46330932474
DeepCCS[M+Na]+126.29930932474

Predicted Kovats Retention Indices

Not Available
Spectra
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 IDFDB030359
KNApSAcK IDNot Available
Chemspider ID21232457
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID88350
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