Showing metabocard for 1-Deoxy-L-glycero-tetrulose 4-phosphate (MMDBc0031765)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 01:48:25 UTC
Update Date2022-08-31 18:24:28 UTC
Metabolite IDMMDBc0031765
Metabolite Identification
Common Name1-Deoxy-L-glycero-tetrulose 4-phosphate
Description1-deoxy-L-glycero-tetrulose 4-phosphate is an intermediate in the synthesis of riboflavin. It is a substrate for the enzyme 6,7-dimethyl-8-ribityllumazine synthase (RibE) which catalyzes the formation of 6,7-dimethyl-8 ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 1-deoxy-L-glycero-tetrulose 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055eeebae19f8>


  Mrv0541 02241222192D          

 11 10  0  0  0  0            999 V2000
    9.6785   -3.6958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3942   -4.1072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9668   -4.1072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6785   -2.8722    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1093   -3.6958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3942   -4.9307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8250   -4.1072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5394   -2.8697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2539   -4.1072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5394   -3.6947    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.7530   -4.4916    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  2  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7 10  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x000055eeebae19f8>

HMDB0304013
     RDKit          3D
1-deoxy-L-glycero-tetrulose 4-phosphate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -3.0176    0.7042   -0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7827    0.7655    0.3586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4137    1.8593    0.7211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0827   -0.4808    0.6864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7338   -1.5834    0.1362 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3381   -0.5071    0.2079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1107    0.5313    0.6743 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6673    0.3270    0.0289 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.5783   -0.1529    1.1316 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2619    1.7421   -0.6499 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6755   -0.8630   -1.1819 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8658    1.1180   -1.4830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3557   -0.3589   -0.6182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8690    1.2018    0.0519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0900   -0.6100    1.7842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1718   -2.3952    0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3887   -0.5057   -0.9043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7980   -1.4534    0.5989 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4628    2.3628    0.0917 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1016   -1.7016   -0.8750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  1 12  1  0
  1 13  1  0
  1 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
 10 19  1  0
 11 20  1  0
M  END
Download

3D SDF for #<Metabolite:0x000055eeebae19f8>


  Mrv0541 02241222192D          

 11 10  0  0  0  0            999 V2000
    9.6785   -3.6958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3942   -4.1072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9668   -4.1072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6785   -2.8722    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1093   -3.6958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3942   -4.9307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8250   -4.1072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5394   -2.8697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2539   -4.1072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5394   -3.6947    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.7530   -4.4916    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  2  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7 10  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031765

> <DATABASE_NAME>
MIME

> <SMILES>
CC(=O)C(O)COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9O6P/c1-3(5)4(6)2-10-11(7,8)9/h4,6H,2H2,1H3,(H2,7,8,9)

> <INCHI_KEY>
OKYHYXLCTGGOLM-UHFFFAOYSA-N

> <FORMULA>
C4H9O6P

> <MOLECULAR_WEIGHT>
184.0844

> <EXACT_MASS>
184.013674532

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.380678488641951

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2-hydroxy-3-oxobutoxy)phosphonic acid

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-1.3126799933333335

> <ALOGPS_LOGS>
-0.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.415057530560526

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.388886854275381

> <JCHEM_PKA_STRONGEST_BASIC>
-3.847198471680728

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
34.8075

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-oxobutyl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x000055eeebae19f8>

HMDB0304013
     RDKit          3D
1-deoxy-L-glycero-tetrulose 4-phosphate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -3.0176    0.7042   -0.4648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7827    0.7655    0.3586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4137    1.8593    0.7211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0827   -0.4808    0.6864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7338   -1.5834    0.1362 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3381   -0.5071    0.2079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1107    0.5313    0.6743 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6673    0.3270    0.0289 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.5783   -0.1529    1.1316 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2619    1.7421   -0.6499 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6755   -0.8630   -1.1819 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8658    1.1180   -1.4830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3557   -0.3589   -0.6182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8690    1.2018    0.0519 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0900   -0.6100    1.7842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1718   -2.3952    0.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3887   -0.5057   -0.9043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7980   -1.4534    0.5989 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4628    2.3628    0.0917 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1016   -1.7016   -0.8750 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  1 12  1  0
  1 13  1  0
  1 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
 10 19  1  0
 11 20  1  0
M  END
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PDB for #<Metabolite:0x000055eeebae19f8>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      18.067  -6.899   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.403  -7.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.738  -7.667   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      18.067  -5.361   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      20.737  -6.899   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      19.403  -9.204   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      22.073  -7.667   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      23.407  -5.357   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      24.741  -7.667   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0      23.407  -6.897   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      23.806  -8.384   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    2    7                                                       
CONECT    6    2                                                            
CONECT    7    5   10                                                       
CONECT    8   10                                                            
CONECT    9   10                                                            
CONECT   10    7    8    9   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 #<Metabolite:0x000055eeebae19f8>

COMPND    HMDB0304013
HETATM    1  C1  UNL     1      -3.018   0.704  -0.465  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.783   0.765   0.359  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.414   1.859   0.721  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.083  -0.481   0.686  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.734  -1.583   0.136  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.338  -0.507   0.208  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.111   0.531   0.674  1.00  0.00           O  
HETATM    8  P1  UNL     1       2.667   0.327   0.029  1.00  0.00           P  
HETATM    9  O4  UNL     1       3.578  -0.153   1.132  1.00  0.00           O  
HETATM   10  O5  UNL     1       3.262   1.742  -0.650  1.00  0.00           O  
HETATM   11  O6  UNL     1       2.675  -0.863  -1.182  1.00  0.00           O  
HETATM   12  H1  UNL     1      -2.866   1.118  -1.483  1.00  0.00           H  
HETATM   13  H2  UNL     1      -3.356  -0.359  -0.618  1.00  0.00           H  
HETATM   14  H3  UNL     1      -3.869   1.202   0.052  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.090  -0.610   1.784  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.172  -2.395   0.168  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.389  -0.506  -0.904  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.798  -1.453   0.599  1.00  0.00           H  
HETATM   19  H8  UNL     1       3.463   2.363   0.092  1.00  0.00           H  
HETATM   20  H9  UNL     1       3.102  -1.702  -0.875  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    3    4
CONECT    4    5    6   15
CONECT    5   16
CONECT    6    7   17   18
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   10   19
CONECT   11   20
END
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SMILES for #<Metabolite:0x000055eeebae19f8>

CC(=O)C(O)COP(O)(O)=O
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INCHI for #<Metabolite:0x000055eeebae19f8>

InChI=1S/C4H9O6P/c1-3(5)4(6)2-10-11(7,8)9/h4,6H,2H2,1H3,(H2,7,8,9)
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Synonyms
ValueSource
3,4-Dihydroxy-2-butanone 4-phosphateChEBI
2-Hydroxy-3-oxobutyl phosphateKegg
3,4-Dihydroxy-2-butanone 4-phosphoric acidGenerator
2-Hydroxy-3-oxobutyl phosphoric acidGenerator
1-Deoxy-L-glycero-tetrulose 4-phosphoric acidGenerator
1-Deoxy-L-glycero-tetrulose 4-phosphateChEBI
L-3,4-Dihydroxybutan-2-one 4-phosphoric acidGenerator
Molecular FormulaC4H9O6P
Average Mass184.0844
Monoisotopic Mass184.013674532
IUPAC Name(2-hydroxy-3-oxobutoxy)phosphonic acid
Traditional Name2-hydroxy-3-oxobutyl phosphate
CAS Registry NumberNot Available
SMILES
CC(=O)C(O)COP(O)(O)=O
InChI Identifier
InChI=1S/C4H9O6P/c1-3(5)4(6)2-10-11(7,8)9/h4,6H,2H2,1H3,(H2,7,8,9)
InChI KeyOKYHYXLCTGGOLM-UHFFFAOYSA-N