Showing NP-Card for (2R)-2-Hydroxy-3-(phosphonatooxy)propanoate (NP0000856)

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Record Information
Version2.0
Created at2013-05-09 21:01:49 UTC
Updated at2024-09-17 15:43:11 UTC
NP-MRD IDNP0000856
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2R)-2-Hydroxy-3-(phosphonatooxy)propanoate
Description(2R)-2-Hydroxy-3-(phosphonatooxy)propanoate, also known as 3-phospho-(R)-glycerate or D-glycerate 3-phosphate, 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 (2R)-2-Hydroxy-3-(phosphonatooxy)propanoate is a drug (2R)-2-hydroxy-3-(phosphonatooxy)propanoate has been detected, but not quantified, in several different foods, such as poppies, small-leaf lindens, lupines, pomegranates, and kombus. These are compounds containing a saccharide unit which bears a carboxylic acid group.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

  Mrv1652309042000402D          

 11 10  0  0  1  0            999 V2000
    8.7751   -4.3490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0582   -3.9350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3446   -4.3490    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6310   -3.9350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3446   -5.1770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9142   -4.3490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6310   -3.1102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4896   -3.9365    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.2040   -4.3490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4896   -3.1115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4896   -4.7615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  1  0  0  0
  4  6  1  0  0  0  0
  4  7  2  0  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  8 11  1  0  0  0  0
M  END
Download

3D MOL for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

HMDB0060180
     RDKit          3D
D-Glycerate 3-phosphate
 18 17  0  0  0  0  0  0  0  0999 V2000
   -3.4602   -0.4318    0.7396 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5644    0.3283    0.3267 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5442    1.6350    0.7566 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5489   -0.1859   -0.6100 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7747   -1.5183   -0.8946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1929    0.0039    0.0620 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8408   -0.4353   -0.7490 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2859   -0.1798    0.0879 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.0208   -0.3569    1.5848 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8030    1.4189   -0.1742 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4974   -1.2044   -0.4390 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3488    2.4351    0.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5538    0.3705   -1.5813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0701   -2.0168   -0.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0971    1.0517    0.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.6492    0.9682 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6878    1.5498    0.2548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2301   -1.8148   -1.1465 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
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  0
  6 16  1  0
 10 17  1  0
 11 18  1  0
M  END
Download

3D SDF for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

  Mrv1652309042000402D          

 11 10  0  0  1  0            999 V2000
    8.7751   -4.3490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0582   -3.9350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3446   -4.3490    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6310   -3.9350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3446   -5.1770    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9142   -4.3490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6310   -3.1102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4896   -3.9365    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.2040   -4.3490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4896   -3.1115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4896   -4.7615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  1  0  0  0
  4  6  1  0  0  0  0
  4  7  2  0  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  8 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000856

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H](COP(O)(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1

> <INCHI_KEY>
OSJPPGNTCRNQQC-UWTATZPHSA-N

> <FORMULA>
C3H7O7P

> <MOLECULAR_WEIGHT>
186.0572

> <EXACT_MASS>
185.99293909

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.540840192774787

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-3-(phosphonooxy)propanoic acid

> <ALOGPS_LOGP>
-2.26

> <JCHEM_LOGP>
-1.642305516

> <ALOGPS_LOGS>
-0.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.4930984077105847

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3022122249394057

> <JCHEM_PKA_STRONGEST_BASIC>
-4.151933713507117

> <JCHEM_POLAR_SURFACE_AREA>
124.29

> <JCHEM_REFRACTIVITY>
31.256400000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-glycerate 3-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

HMDB0060180
     RDKit          3D
D-Glycerate 3-phosphate
 18 17  0  0  0  0  0  0  0  0999 V2000
   -3.4602   -0.4318    0.7396 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5644    0.3283    0.3267 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5442    1.6350    0.7566 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5489   -0.1859   -0.6100 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7747   -1.5183   -0.8946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1929    0.0039    0.0620 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8408   -0.4353   -0.7490 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2859   -0.1798    0.0879 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.0208   -0.3569    1.5848 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8030    1.4189   -0.1742 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4974   -1.2044   -0.4390 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3488    2.4351    0.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5538    0.3705   -1.5813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0701   -2.0168   -0.0900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0971    1.0517    0.3405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.6492    0.9682 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6878    1.5498    0.2548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2301   -1.8148   -1.1465 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
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  0
  6 16  1  0
 10 17  1  0
 11 18  1  0
M  END
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PDB for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0      16.380  -8.118   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      15.042  -7.345   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.710  -8.118   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.378  -7.345   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      13.710  -9.664   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      11.040  -8.118   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      12.378  -5.806   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0      17.714  -7.348   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      19.047  -8.118   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      17.714  -5.808   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.714  -8.888   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3    6    7                                                  
CONECT    5    3                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    1    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

COMPND    HMDB0060180
HETATM    1  O1  UNL     1      -3.460  -0.432   0.740  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.564   0.328   0.327  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.544   1.635   0.757  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.549  -0.186  -0.610  1.00  0.00           C  
HETATM    5  O3  UNL     1      -1.775  -1.518  -0.895  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.193   0.004   0.062  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.841  -0.435  -0.749  1.00  0.00           O  
HETATM    8  P1  UNL     1       2.286  -0.180   0.088  1.00  0.00           P  
HETATM    9  O5  UNL     1       2.021  -0.357   1.585  1.00  0.00           O  
HETATM   10  O6  UNL     1       2.803   1.419  -0.174  1.00  0.00           O  
HETATM   11  O7  UNL     1       3.497  -1.204  -0.439  1.00  0.00           O  
HETATM   12  H1  UNL     1      -2.349   2.435   0.168  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.554   0.370  -1.581  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.070  -2.017  -0.090  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.097   1.052   0.341  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.211  -0.649   0.968  1.00  0.00           H  
HETATM   17  H6  UNL     1       3.688   1.550   0.255  1.00  0.00           H  
HETATM   18  H7  UNL     1       3.230  -1.815  -1.147  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7   15   16
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   10   17
CONECT   11   18
END
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SMILES for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

O[C@H](COP(O)(O)=O)C(O)=O
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INCHI for NP0000856 ((2R)-2-Hydroxy-3-(phosphonatooxy)propanoate)

InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
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View in JSmolView NMR Assignments
Synonyms
Chemical FormulaC3H7O7P
Average Mass186.0572 Da
Monoisotopic Mass185.99294 Da
IUPAC Name(2R)-2-hydroxy-3-(phosphonooxy)propanoic acid
Traditional NameD-glycerate 3-phosphate
CAS Registry NumberNot Available
SMILES
O[C@H](COP(O)(O)=O)C(O)=O
InChI Identifier
InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
InChI KeyOSJPPGNTCRNQQC-UWTATZPHSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
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
  • Glyceric_acid
  • Monoalkyl phosphate
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Carboxylic acid
  • Alcohol
  • Carbonyl group
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility21 g/LALOGPS
logP-2.3ALOGPS
logP-1.6ChemAxon
logS-0.95ALOGPS
pKa (Strongest Acidic)1.3ChemAxon
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area124.29 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.26 m³·mol⁻¹ChemAxon
Polarizability13.54 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0060180
DrugBank IDDB04510
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030460
KNApSAcK IDC00019551
Chemspider ID388326
KEGG Compound IDC00197
BioCyc IDG3P
BiGG IDNot Available
Wikipedia Link3-Phosphoglyceric_acid
METLIN IDNot Available
PubChem Compound439183
PDB IDNot Available
ChEBI ID17794
Good Scents IDNot Available
References
General References
  1. Bartsch O, Hagemann M, Bauwe H: Only plant-type (GLYK) glycerate kinases produce d-glycerate 3-phosphate. FEBS Lett. 2008 Sep 3;582(20):3025-8. doi: 10.1016/j.febslet.2008.07.038. Epub 2008 Aug 7. [PubMed:18675808 ]
  2. Brechtel E, Huwig A, Giffhorn F: L-glucitol catabolism in Stenotrophomonas maltophilia Ac. Appl Environ Microbiol. 2002 Feb;68(2):582-7. doi: 10.1128/AEM.68.2.582-587.2002. [PubMed:11823194 ]