Showing metabocard for 3-Phospho-D-glycerate (MMDBc0031724)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 01:45:54 UTC
Update Date2022-08-31 18:23:57 UTC
Metabolite IDMMDBc0031724
Metabolite Identification
Common Name3-Phospho-D-glycerate
Description3-phospho-D-glycerate is a member of the chemical class known as Sugar Acids and Derivatives. These are compounds containing a saccharide unit which bears a carboxylic acid group.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560bdfbddc38>


  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
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3D MOL for #<Metabolite:0x0000560bdfbddc38>

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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3D SDF for #<Metabolite:0x0000560bdfbddc38>


  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>
MMDBc0031724

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x0000560bdfbddc38>

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 #<Metabolite:0x0000560bdfbddc38>

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 #<Metabolite:0x0000560bdfbddc38>

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 #<Metabolite:0x0000560bdfbddc38>

O[C@H](COP(O)(O)=O)C(O)=O
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INCHI for #<Metabolite:0x0000560bdfbddc38>

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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Synonyms
ValueSource
3-Phospho-(R)-glycerateChEBI
3-Phospho-D-glycerateChEBI
3-PhosphoglycerateChEBI
3-Phospho-(R)-glyceric acidGenerator
3-Phospho-D-glyceric acidGenerator
3-Phosphoglyceric acidGenerator
D-Glyceric acid 3-phosphoric acidGenerator
(2R)-2-Hydroxy-3-(phosphonatooxy)propanoic acidHMDB
(2R)-2-Hydroxy-3-(phosphonooxy)propanoic acidHMDB
2-Hydroxy-3-(phosphonatooxy)propanoateHMDB
D-(-)-3-Phosphoglyceric acidHMDB
D-3-Phosphoglyceric acidHMDB
D-Glyceric acid 3-phosphateHMDB
Glycerate 3-phosphateMeSH
3-Phosphoglycerate, trisodium saltMeSH
3-Phosphoglycerate, monosodium saltMeSH
3-Phosphoglycerate, (R)-isomerMeSH
D-Glycerate 3-phosphateChEBI
Molecular FormulaC3H7O7P
Average Mass186.0572
Monoisotopic Mass185.99293909
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