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Showing metabocard for 3-Phosphoglyceric acid (HMDB0000807)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:11 UTC
HMDB IDHMDB0000807
Secondary Accession Numbers
  • HMDB00807
Metabolite Identification
Common Name3-Phosphoglyceric acid
Description3-Phosphoglyceric acid, also known as 3PG, 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. 3PG is the conjugate acid of glycerate 3-phosphate (GP or G3P). It is a solid that is soluble in water. 3-Phosphoglyceric acid exists in all living species, ranging from bacteria to humans. The glycerate is a biochemically significant metabolic intermediate in both glycolysis and the Calvin cycle. This is the first compound formed during the C3 or Calvin cycle. Glycerate 3-phosphate is also a precursor for serine, which, in turn, can create cysteine and glycine through the homocysteine cycle. Within humans, 3-phosphoglyceric acid participates in a number of enzymatic reactions. In particular, 3-phosphoglyceric acid can be biosynthesized from glyceric acid 1,3-biphosphate, which is mediated by the enzyme phosphoglycerate kinase 1. In addition, 3PG can be converted into 2-phospho-D-glyceric acid, which is catalyzed by the enzyme phosphoglycerate mutase 2. 3-phosphoglyceric acid is involved in the Warburg effect (aerobic glycolysis), a metabolic shift that is a hallmark of cancer (PMID: 29362480 ).
Structure
Data?1676999711
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000807 (3-Phosphoglyceric acid)


  Mrv1652309042000132D          

 11 10  0  0  0  0            999 V2000
   26.0261  -21.4788    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.7406  -21.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.1695  -20.2413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.3116  -21.8913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.6136  -20.7644    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.5985  -21.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4386  -22.1933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.8841  -22.3039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4551  -21.4788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.1695  -21.0663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8841  -21.4788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  2  0  0  0  0
  2  9  1  0  0  0  0
  3 10  1  0  0  0  0
  6 11  1  0  0  0  0
  8 11  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
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3D MOL for HMDB0000807 (3-Phosphoglyceric acid)

HMDB0000807
     RDKit          3D
3-Phosphoglyceric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    3.4971    0.0150    0.9347 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5850   -0.0922    0.0763 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7393    0.4083   -1.2075 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3179   -0.7569    0.4113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2952   -1.2119    1.7296 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1217    0.1972    0.2783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9996   -0.5416    0.5618 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4366    0.2775    0.4838 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.8169    0.8882    1.8317 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098    1.4236   -0.7448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6697   -0.8628    0.1439 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7615    1.4149   -1.3159 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0782   -1.6000   -0.2994 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7753   -2.0451    1.8671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125    0.7090   -0.6911 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3208    0.9978    1.0461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8101    2.0997   -0.6318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3617   -1.3206   -0.6987 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  0
  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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3D SDF for HMDB0000807 (3-Phosphoglyceric acid)


  Mrv1652309042000132D          

 11 10  0  0  0  0            999 V2000
   26.0261  -21.4788    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.7406  -21.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.1695  -20.2413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.3116  -21.8913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.6136  -20.7644    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.5985  -21.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4386  -22.1933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.8841  -22.3039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4551  -21.4788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.1695  -21.0663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.8841  -21.4788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  2  0  0  0  0
  2  9  1  0  0  0  0
  3 10  1  0  0  0  0
  6 11  1  0  0  0  0
  8 11  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000807

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(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)

> <INCHI_KEY>
OSJPPGNTCRNQQC-UHFFFAOYSA-N

> <FORMULA>
C3H7O7P

> <MOLECULAR_WEIGHT>
186.0572

> <EXACT_MASS>
185.99293909

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.290097380266747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
1.3022122249394052

> <JCHEM_PKA_STRONGEST_BASIC>
-4.151933713507117

> <JCHEM_POLAR_SURFACE_AREA>
124.28999999999999

> <JCHEM_REFRACTIVITY>
31.256400000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phosphoglycerate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000807 (3-Phosphoglyceric acid)

HMDB0000807
     RDKit          3D
3-Phosphoglyceric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    3.4971    0.0150    0.9347 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5850   -0.0922    0.0763 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7393    0.4083   -1.2075 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3179   -0.7569    0.4113 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2952   -1.2119    1.7296 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1217    0.1972    0.2783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9996   -0.5416    0.5618 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4366    0.2775    0.4838 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.8169    0.8882    1.8317 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098    1.4236   -0.7448 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6697   -0.8628    0.1439 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7615    1.4149   -1.3159 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0782   -1.6000   -0.2994 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7753   -2.0451    1.8671 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125    0.7090   -0.6911 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3208    0.9978    1.0461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8101    2.0997   -0.6318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3617   -1.3206   -0.6987 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  0
  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 HMDB0000807 (3-Phosphoglyceric acid)

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  P   UNK     0      48.582 -40.094   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      49.916 -39.324   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      52.583 -37.784   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      47.248 -40.864   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      47.812 -38.760   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      55.251 -39.324   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      49.352 -41.427   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      53.917 -41.634   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      51.250 -40.094   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      52.583 -39.324   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      53.917 -40.094   0.000  0.00  0.00           C+0
CONECT    1    2    4    5    7                                             
CONECT    2    1    9                                                       
CONECT    3   10                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6   11                                                            
CONECT    7    1                                                            
CONECT    8   11                                                            
CONECT    9    2   10                                                       
CONECT   10    3    9   11                                                  
CONECT   11    6    8   10                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0000807 (3-Phosphoglyceric acid)

COMPND    HMDB0000807
HETATM    1  O1  UNL     1       3.497   0.015   0.935  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.585  -0.092   0.076  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.739   0.408  -1.207  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.318  -0.757   0.411  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.295  -1.212   1.730  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.122   0.197   0.278  1.00  0.00           C  
HETATM    7  O4  UNL     1      -1.000  -0.542   0.562  1.00  0.00           O  
HETATM    8  P1  UNL     1      -2.437   0.278   0.484  1.00  0.00           P  
HETATM    9  O5  UNL     1      -2.817   0.888   1.832  1.00  0.00           O  
HETATM   10  O6  UNL     1      -2.510   1.424  -0.745  1.00  0.00           O  
HETATM   11  O7  UNL     1      -3.670  -0.863   0.144  1.00  0.00           O  
HETATM   12  H1  UNL     1       2.761   1.415  -1.316  1.00  0.00           H  
HETATM   13  H2  UNL     1       1.078  -1.600  -0.299  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.775  -2.045   1.867  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.112   0.709  -0.691  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.321   0.998   1.046  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.810   2.100  -0.632  1.00  0.00           H  
HETATM   18  H7  UNL     1      -3.362  -1.321  -0.699  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 HMDB0000807 (3-Phosphoglyceric acid)

OC(COP(O)(O)=O)C(O)=O
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INCHI for HMDB0000807 (3-Phosphoglyceric acid)

InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-(Dihydrogen phosphate)glycerateChEBI
3-(Dihydrogen phosphate)glyceric acidChEBI
3-PhosphoglycerateChEBI
DL-Glycerate 3-phosphateChEBI
Glycerate 3-phosphateChEBI
Glycerate 3-phosphatesChEBI
Glyceric acid 3-phosphateChEBI
3-(Dihydrogen phosphoric acid)glyceric acidGenerator
DL-Glyceric acid 3-phosphoric acidGenerator
Glyceric acid 3-phosphoric acidGenerator
Glyceric acid 3-phosphatesGenerator
3-GlycerophosphorateHMDB
3-Glycerophosphoric acidHMDB
3-p-D-GlycerateHMDB
3-p-GlycerateHMDB
3-PGHMDB
3-PGAHMDB
3-Phospho-(R)-glycerateHMDB
3-Phospho-D-glycerateHMDB
3-Phospho-glycerateHMDB
3-Phospho-glyceric acidHMDB
D-(-)-3-Phosphoglyceric acidHMDB
D-Glycerate 3-phosphateHMDB
G3PHMDB
Glycerate-3-pHMDB
PhosphoglycerateHMDB
3-Phosphoglycerate, trisodium saltHMDB
3-Phosphoglycerate, (R)-isomerHMDB
3-Phosphoglycerate, monosodium saltHMDB
Chemical FormulaC3H7O7P
Average Molecular Weight186.0572
Monoisotopic Molecular Weight185.99293909
IUPAC Name2-hydroxy-3-(phosphonooxy)propanoic acid
Traditional Namephosphoglycerate
CAS Registry Number820-11-1
SMILES
OC(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)
InChI KeyOSJPPGNTCRNQQC-UHFFFAOYSA-N
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
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Astarita_neg126.030932474
[M-H]-Baker125.60530932474
[M-H]-Not Available125.605http://allccs.zhulab.cn/database/detail?ID=AllCCS00000415
[M+H]+Not Available136.4http://allccs.zhulab.cn/database/detail?ID=AllCCS00000415
Predicted Molecular 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
Polarizability13.29 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
DarkChem[M+H]+139.3531661259
DarkChem[M-H]-131.61131661259
AllCCS[M+H]+140.69532859911
AllCCS[M-H]-130.34532859911
DeepCCS[M+H]+126.49230932474
DeepCCS[M-H]-122.81630932474
DeepCCS[M-2H]-160.17430932474
DeepCCS[M+Na]+135.20130932474
AllCCS[M+H]+140.732859911
AllCCS[M+H-H2O]+136.932859911
AllCCS[M+NH4]+144.232859911
AllCCS[M+Na]+145.232859911
AllCCS[M-H]-130.332859911
AllCCS[M+Na-2H]-132.232859911
AllCCS[M+HCOO]-134.332859911

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, 2022.1.87 minutes32390414
Predicted by Siyang on May 30, 20229.4482 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20228.97 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid439.4 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid488.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid348.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid33.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid226.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid106.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid305.4 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 Acid219.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)851.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid592.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid42.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid667.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid215.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid361.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate782.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA391.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water501.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Phosphoglyceric acidOC(COP(O)(O)=O)C(O)=O2741.0Standard polar33892256
3-Phosphoglyceric acidOC(COP(O)(O)=O)C(O)=O1410.2Standard non polar33892256
3-Phosphoglyceric acidOC(COP(O)(O)=O)C(O)=O1692.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Phosphoglyceric acid,1TMS,isomer #1C[Si](C)(C)OC(COP(=O)(O)O)C(=O)O1733.1Semi standard non polar33892256
3-Phosphoglyceric acid,1TMS,isomer #2C[Si](C)(C)OC(=O)C(O)COP(=O)(O)O1699.7Semi standard non polar33892256
3-Phosphoglyceric acid,1TMS,isomer #3C[Si](C)(C)OP(=O)(O)OCC(O)C(=O)O1720.8Semi standard non polar33892256
3-Phosphoglyceric acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O)O)O[Si](C)(C)C1738.7Semi standard non polar33892256
3-Phosphoglyceric acid,2TMS,isomer #2C[Si](C)(C)OC(COP(=O)(O)O[Si](C)(C)C)C(=O)O1773.9Semi standard non polar33892256
3-Phosphoglyceric acid,2TMS,isomer #3C[Si](C)(C)OC(=O)C(O)COP(=O)(O)O[Si](C)(C)C1715.2Semi standard non polar33892256
3-Phosphoglyceric acid,2TMS,isomer #4C[Si](C)(C)OP(=O)(OCC(O)C(=O)O)O[Si](C)(C)C1764.3Semi standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C1778.9Semi standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C1756.7Standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O)O[Si](C)(C)C)O[Si](C)(C)C2134.9Standard polar33892256
3-Phosphoglyceric acid,3TMS,isomer #2C[Si](C)(C)OC(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(=O)O1803.7Semi standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #2C[Si](C)(C)OC(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(=O)O1791.5Standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #2C[Si](C)(C)OC(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(=O)O2004.4Standard polar33892256
3-Phosphoglyceric acid,3TMS,isomer #3C[Si](C)(C)OC(=O)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1754.1Semi standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #3C[Si](C)(C)OC(=O)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1746.7Standard non polar33892256
3-Phosphoglyceric acid,3TMS,isomer #3C[Si](C)(C)OC(=O)C(O)COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C1947.9Standard polar33892256
3-Phosphoglyceric acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C1833.3Semi standard non polar33892256
3-Phosphoglyceric acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C1819.9Standard non polar33892256
3-Phosphoglyceric acid,4TMS,isomer #1C[Si](C)(C)OC(=O)C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C1902.5Standard polar33892256
3-Phosphoglyceric acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(COP(=O)(O)O)C(=O)O1959.6Semi standard non polar33892256
3-Phosphoglyceric acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)C(O)COP(=O)(O)O1927.5Semi standard non polar33892256
3-Phosphoglyceric acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OP(=O)(O)OCC(O)C(=O)O1953.2Semi standard non polar33892256
3-Phosphoglyceric acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O)O)O[Si](C)(C)C(C)(C)C2126.7Semi standard non polar33892256
3-Phosphoglyceric acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(=O)O2153.1Semi standard non polar33892256
3-Phosphoglyceric acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(O)COP(=O)(O)O[Si](C)(C)C(C)(C)C2124.7Semi standard non polar33892256
3-Phosphoglyceric acid,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OP(=O)(OCC(O)C(=O)O)O[Si](C)(C)C(C)(C)C2174.8Semi standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2349.8Semi standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2389.7Standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2438.1Standard polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(=O)O2376.2Semi standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(=O)O2347.6Standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(=O)O2335.6Standard polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(O)COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2366.5Semi standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(O)COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2367.3Standard non polar33892256
3-Phosphoglyceric acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C(O)COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2293.3Standard polar33892256
3-Phosphoglyceric acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2587.9Semi standard non polar33892256
3-Phosphoglyceric acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2530.9Standard non polar33892256
3-Phosphoglyceric acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2336.2Standard polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Cellular Cytoplasm
  • Saliva
  • Urine
Tissue Locations
  • Placenta
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified58.2 +/- 14.4 uMNewborn (0-30 days old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified47.2 +/- 7.4 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Cellular CytoplasmDetected and Quantified45 uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified6.34 +/- 3.26 uMAdult (>18 years old)FemaleNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected and Quantified6.07 +/- 3.08 uMAdult (>18 years old)MaleAlzheimer's disease details
SalivaDetected and Quantified7.73 +/- 6.31 uMAdult (>18 years old)MaleFrontotemporal lobe dementia details
SalivaDetected and Quantified8.40 +/- 9.51 uMAdult (>18 years old)BothLewy body disease details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Bladder cancer		 details
Associated Disorders and Diseases
Disease References
Alzheimer's disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022255
KNApSAcK IDC00007286
Chemspider ID704
KEGG Compound IDC00597
BioCyc IDNot Available
BiGG ID34230
Wikipedia Link3-Phosphoglyceric_acid
METLIN ID150
PubChem Compound724
PDB IDNot Available
ChEBI ID17050
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceJakoby, Wm. B.; Brummond, Dewey O.; Ochoa, Severo. Formation of 3-phosphoglyceric acid by carbon dioxide fixation with spinach-leaf enzymes. Journal of Biological Chemistry (1956), 218 811-22.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2:18. [PubMed:15882454 ]
  3. Yu KT, Pendley C 2nd, Herczeg T, Pendleton RG: 2,3-Diphosphoglycerate phosphatase/synthase: a potential target for elevating the diphosphoglycerate level in human red blood cells. J Pharmacol Exp Ther. 1990 Jan;252(1):192-200. [PubMed:2153800 ]
  4. Uchida K, Kondoh K, Matuo Y: Recombinant M-, B- and MB-type isozymes of human phosphoglyceric acid mutase: their large-scale production and preparation of polyclonal antibodies specific to M- and B-type isozymes. Clin Chim Acta. 1995 Jun 15;237(1-2):43-58. [PubMed:7664478 ]
  5. Uchida K, Mori K, Matuo Y: [Phosphoglyceric acid mutase]. Nihon Rinsho. 1995 May;53(5):1247-52. [PubMed:7602787 ]
  6. Nakai A, Shigematsu Y, Liu YY, Kikawa Y, Sudo M: Urinary sugar phosphates and related organic acids in fructose-1,6-diphosphatase deficiency. J Inherit Metab Dis. 1993;16(2):408-14. [PubMed:8412001 ]
  7. Sayed A, Matsuyama S, Inoue K, Alsina J, Cai F, Chen J, Inouye M: ATPase and GTPase activities copurifying with GTP-binding proteins in E. coli. J Mol Microbiol Biotechnol. 2000 Jul;2(3):261-3. [PubMed:10937433 ]
  8. Grisolia S, Salinas M, Wallace R, Singh GK: Influence of size, protein concentration, protein synthesis inhibitors,and carbon on clearance of enzymes and proteins from blood. Physiol Chem Phys. 1976;8(1):37-52. [PubMed:183226 ]
  9. Mair J: Progress in myocardial damage detection: new biochemical markers for clinicians. Crit Rev Clin Lab Sci. 1997;34(1):1-66. [PubMed:9055056 ]
  10. Glaus M, Schneider W: Iron release from transferrin induced by mixed ligand complexes of copper(II). Biol Met. 1989;2(3):185-90. [PubMed:2490073 ]
  11. Veech RL, Lawson JW, Cornell NW, Krebs HA: Cytosolic phosphorylation potential. J Biol Chem. 1979 Jul 25;254(14):6538-47. [PubMed:36399 ]
  12. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
  13. Sun Q, Li S, Wang Y, Peng H, Zhang X, Zheng Y, Li C, Li L, Chen R, Chen X, Bai W, Jiang X, Liu L, Wei F, Wang B, Zhang Y, Li H, Ren X, Zhang H: Phosphoglyceric acid mutase-1 contributes to oncogenic mTOR-mediated tumor growth and confers non-small cell lung cancer patients with poor prognosis. Cell Death Differ. 2018 Jun;25(6):1160-1173. doi: 10.1038/s41418-017-0034-y. Epub 2018 Jan 23. [PubMed:29362480 ]
  14. (). Mayo Medical Laboratories 2005 Test Catalog. .

Only showing the first 10 proteins. There are 11 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Bisphosphoglycerate mutase
General function:
Involved in catalytic activity
Specific function:
Plays a major role in regulating hemoglobin oxygen affinity by controlling the levels of its allosteric effector 2,3-bisphosphoglycerate (2,3-BPG). Also exhibits mutase (EC 5.4.2.1) and phosphatase (EC 3.1.3.13) activities.
Gene Name:
BPGM
Uniprot ID:
P07738
Molecular weight:
30004.98
Reactions
2-Phospho-D-glyceric acid → 3-Phosphoglyceric aciddetails
2,3-Diphosphoglyceric acid + Water → 3-Phosphoglyceric acid + Phosphatedetails
Enzyme Details
2. Phosphoglycerate mutase 2
General function:
Involved in catalytic activity
Specific function:
Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also catalyze the reaction of EC 5.4.2.4 (synthase) and EC 3.1.3.13 (phosphatase), but with a reduced activity.
Gene Name:
PGAM2
Uniprot ID:
P15259
Molecular weight:
28765.96
Reactions
2-Phospho-D-glyceric acid → 3-Phosphoglyceric aciddetails
2,3-Diphosphoglyceric acid + Water → 3-Phosphoglyceric acid + Phosphatedetails
Enzyme Details
3. Probable phosphoglycerate mutase 4
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PGAM4
Uniprot ID:
Q8N0Y7
Molecular weight:
28776.605
Reactions
2-Phospho-D-glyceric acid → 3-Phosphoglyceric aciddetails
2,3-Diphosphoglyceric acid + Water → 3-Phosphoglyceric acid + Phosphatedetails
3-Phosphoglyceric acid → 2-Phospho-D-glyceric aciddetails
Enzyme Details
4. Phosphoglycerate mutase 1
General function:
Involved in catalytic activity
Specific function:
Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also catalyze the reaction of EC 5.4.2.4 (synthase) and EC 3.1.3.13 (phosphatase), but with a reduced activity.
Gene Name:
PGAM1
Uniprot ID:
P18669
Molecular weight:
28803.675
Reactions
2-Phospho-D-glyceric acid → 3-Phosphoglyceric aciddetails
2,3-Diphosphoglyceric acid + Water → 3-Phosphoglyceric acid + Phosphatedetails
Enzyme Details
5. Acylphosphatase-2
General function:
Involved in acylphosphatase activity
Specific function:
Its physiological role is not yet clear.
Gene Name:
ACYP2
Uniprot ID:
P14621
Molecular weight:
11139.52
Reactions
Glyceric acid 1,3-biphosphate + Water → 3-Phosphoglyceric acid + Phosphatedetails
Enzyme Details
6. Acylphosphatase-1
General function:
Involved in acylphosphatase activity
Specific function:
Its physiological role is not yet clear.
Gene Name:
ACYP1
Uniprot ID:
P07311
Molecular weight:
11260.84
Reactions
Glyceric acid 1,3-biphosphate + Water → 3-Phosphoglyceric acid + Phosphatedetails
Enzyme Details
7. D-3-phosphoglycerate dehydrogenase
General function:
Involved in phosphoglycerate dehydrogenase activity
Specific function:
Not Available
Gene Name:
PHGDH
Uniprot ID:
O43175
Molecular weight:
56650.03
Reactions
3-Phosphoglyceric acid + NAD → Phosphohydroxypyruvic acid + NADHdetails
3-Phosphoglyceric acid + NAD → Phosphohydroxypyruvic acid + NADH + Hydrogen Iondetails
Enzyme Details
8. Phosphoglycerate kinase 2
General function:
Carbohydrate transport and metabolism
Specific function:
Not Available
Gene Name:
PGK2
Uniprot ID:
P07205
Molecular weight:
44795.79
Reactions
Adenosine triphosphate + 3-Phosphoglyceric acid → ADP + Glyceric acid 1,3-biphosphatedetails
Enzyme Details
9. Phosphoglycerate kinase 1
General function:
Involved in phosphoglycerate kinase activity
Specific function:
In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).
Gene Name:
PGK1
Uniprot ID:
P00558
Molecular weight:
44614.36
Reactions
Adenosine triphosphate + 3-Phosphoglyceric acid → ADP + Glyceric acid 1,3-biphosphatedetails
Enzyme Details
10. Glycerate kinase
General function:
Carbohydrate transport and metabolism
Specific function:
Not Available
Gene Name:
GLYCTK
Uniprot ID:
Q8IVS8
Molecular weight:
25036.865
Reactions
Adenosine triphosphate + Glyceric acid → ADP + 3-Phosphoglyceric aciddetails

Only showing the first 10 proteins. There are 11 proteins in total.

Show all enzymes and transporters