Showing metabocard for D-Erythrose 4-phosphate (MMDBc0029695)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:37:54 UTC
Update Date2024-04-30 19:40:48 UTC
Metabolite IDMMDBc0029695
Metabolite Identification
Common NameD-Erythrose 4-phosphate
DescriptionD-Erythrose 4-phosphate is a phosphorylated derivative of erythrose that serves as an important intermediate in the pentose phosphate pathway. It is also used in phenylalanine, tyrosine and tryptophan biosynthesis, and it plays a role in vitamin B6 metabolism (KEGG)
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923ef0b7c0>


  Mrv1652307222018152D          

 12 11  0  0  0  0            999 V2000
 9992.1454 9992.7138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9992.8594 9992.3018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.4306 9992.3018    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9992.1454 9993.5385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.5749 9992.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.7158 9992.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.4306 9991.4764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.2904 9992.3018    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9990.0011 9992.3018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8780 9991.5871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.0038 9992.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.7028 9991.5871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  1  0  0  0
  5  8  1  0  0  0  0
  6  9  2  0  0  0  0
  8 10  2  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f923ef0b7c0>

HMDB0001321
     RDKit          3D
D-Erythrose 4-phosphate
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.6345    1.8746   -1.0356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6132    1.0687   -0.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2474   -0.3507   -0.3875 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2793   -1.1153    0.7602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8902   -0.3883   -1.0364 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5789   -1.7185   -1.3717 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2048    0.0771   -0.0988 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3909   -0.0283   -0.8052 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7330    0.4499    0.0834 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8841    0.5980   -0.8960 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1455   -0.7469    1.1986 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5125    1.9326    0.8419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8672    1.4048    0.8678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9724   -0.7477   -1.1276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0252   -2.0430    0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8575    0.2517   -1.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2318   -2.1314   -0.5445 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0072    1.1092    0.2664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2272   -0.5688    0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1980   -1.6059    0.7261 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8944    2.6783    0.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  9 12  1  0
  2 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  6
  6 17  1  0
  7 18  1  0
  7 19  1  0
 11 20  1  0
 12 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f923ef0b7c0>


  Mrv1652307222018152D          

 12 11  0  0  0  0            999 V2000
 9992.1454 9992.7138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9992.8594 9992.3018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.4306 9992.3018    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9992.1454 9993.5385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.5749 9992.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.7158 9992.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9991.4306 9991.4764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.2904 9992.3018    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9990.0011 9992.3018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.8780 9991.5871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.0038 9992.7138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9994.7028 9991.5871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  1  0  0  0
  5  8  1  0  0  0  0
  6  9  2  0  0  0  0
  8 10  2  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029695

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9O7P/c5-1-3(6)4(7)2-11-12(8,9)10/h1,3-4,6-7H,2H2,(H2,8,9,10)/t3-,4+/m0/s1

> <INCHI_KEY>
NGHMDNPXVRFFGS-IUYQGCFVSA-N

> <FORMULA>
C4H9O7P

> <MOLECULAR_WEIGHT>
200.0838

> <EXACT_MASS>
200.008589154

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.408046810674074

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3R)-2,3-dihydroxy-4-oxobutoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.89

> <JCHEM_LOGP>
-2.431256710333334

> <ALOGPS_LOGS>
-0.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.505414511121815

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.479591569624267

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5741525769148197

> <JCHEM_POLAR_SURFACE_AREA>
124.29000000000002

> <JCHEM_REFRACTIVITY>
36.2935

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.37e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-O-phosphono-D-erythrose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f923ef0b7c0>

HMDB0001321
     RDKit          3D
D-Erythrose 4-phosphate
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.6345    1.8746   -1.0356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6132    1.0687   -0.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2474   -0.3507   -0.3875 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2793   -1.1153    0.7602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8902   -0.3883   -1.0364 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5789   -1.7185   -1.3717 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2048    0.0771   -0.0988 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3909   -0.0283   -0.8052 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7330    0.4499    0.0834 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8841    0.5980   -0.8960 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1455   -0.7469    1.1986 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5125    1.9326    0.8419 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8672    1.4048    0.8678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9724   -0.7477   -1.1276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0252   -2.0430    0.5419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8575    0.2517   -1.9250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2318   -2.1314   -0.5445 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0072    1.1092    0.2664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2272   -0.5688    0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1980   -1.6059    0.7261 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8944    2.6783    0.3196 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  9 12  1  0
  2 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  6
  6 17  1  0
  7 18  1  0
  7 19  1  0
 11 20  1  0
 12 21  1  0
M  END
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PDB for #<Metabolite:0x00007f923ef0b7c0>

HEADER    PROTEIN                                 22-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUL-20         0                                  
HETATM    1  C   UNK     0    8652.0058653.066   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8653.3378652.297   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8650.6708652.297   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8652.0058654.605   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8654.6738653.066   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8649.3368653.066   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    8650.6708650.756   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0    8656.0098652.297   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0    8648.0028652.297   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8655.2398650.963   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8657.3418653.066   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8656.7798650.963   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6    7                                                  
CONECT    4    1                                                            
CONECT    5    2    8                                                       
CONECT    6    3    9                                                       
CONECT    7    3                                                            
CONECT    8    5   10   11   12                                             
CONECT    9    6                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    8                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for #<Metabolite:0x00007f923ef0b7c0>

COMPND    HMDB0001321
HETATM    1  O1  UNL     1      -2.635   1.875  -1.036  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.613   1.069  -0.133  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.247  -0.351  -0.388  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.279  -1.115   0.760  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.890  -0.388  -1.036  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.579  -1.718  -1.372  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.205   0.077  -0.099  1.00  0.00           C  
HETATM    8  O4  UNL     1       1.391  -0.028  -0.805  1.00  0.00           O  
HETATM    9  P1  UNL     1       2.733   0.450   0.083  1.00  0.00           P  
HETATM   10  O5  UNL     1       3.884   0.598  -0.896  1.00  0.00           O  
HETATM   11  O6  UNL     1       3.145  -0.747   1.199  1.00  0.00           O  
HETATM   12  O7  UNL     1       2.513   1.933   0.842  1.00  0.00           O  
HETATM   13  H1  UNL     1      -2.867   1.405   0.868  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.972  -0.748  -1.128  1.00  0.00           H  
HETATM   15  H3  UNL     1      -2.025  -2.043   0.542  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.857   0.252  -1.925  1.00  0.00           H  
HETATM   17  H5  UNL     1      -0.232  -2.131  -0.544  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.007   1.109   0.266  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.227  -0.569   0.818  1.00  0.00           H  
HETATM   20  H8  UNL     1       3.198  -1.606   0.726  1.00  0.00           H  
HETATM   21  H9  UNL     1       2.894   2.678   0.320  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   13
CONECT    3    4    5   14
CONECT    4   15
CONECT    5    6    7   16
CONECT    6   17
CONECT    7    8   18   19
CONECT    8    9
CONECT    9   10   10   11   12
CONECT   11   20
CONECT   12   21
END
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SMILES for #<Metabolite:0x00007f923ef0b7c0>

O[C@H](COP(O)(O)=O)[C@@H](O)C=O
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INCHI for #<Metabolite:0x00007f923ef0b7c0>

InChI=1S/C4H9O7P/c5-1-3(6)4(7)2-11-12(8,9)10/h1,3-4,6-7H,2H2,(H2,8,9,10)/t3-,4+/m0/s1
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Synonyms
ValueSource
4-O-Phosphono-D-erythroseChEBI
Erythose-4-phosphateChEBI
D-Erythrose 4-phosphoric acidGenerator
Erythose-4-phosphoric acidGenerator
D-Erythrose 4-PO4HMDB
D-Erythrose-4-PHMDB
D-Erythrose-4-phosphateHMDB
Erythrose 4-phosphateHMDB, MeSH
Erythrose 4-PO4HMDB
Erythrose-4-PHMDB
Erythrose-4-phosphateHMDB
Erythrose-4PHMDB
Threose 4-phosphateHMDB, MeSH
Erythrose 4-phosphate, (r*,r*)-isomerMeSH, HMDB
Erythrose 4-phosphate, ((r*,r*)-(+-))-isomerMeSH, HMDB
(2R,3R)-2,3-Dihydroxy-4-(phosphonooxy)butanalHMDB
D-Erythrose 4-phosphateHMDB
Molecular FormulaC4H9O7P
Average Mass200.0838
Monoisotopic Mass200.008589154
IUPAC Name[(2R,3R)-2,3-dihydroxy-4-oxobutoxy]phosphonic acid
Traditional Name4-O-phosphono-D-erythrose
CAS Registry Number585-18-2
SMILES
O[C@H](COP(O)(O)=O)[C@@H](O)C=O
InChI Identifier
InChI=1S/C4H9O7P/c5-1-3(6)4(7)2-11-12(8,9)10/h1,3-4,6-7H,2H2,(H2,8,9,10)/t3-,4+/m0/s1
InChI KeyNGHMDNPXVRFFGS-IUYQGCFVSA-N