Showing metabocard for D-Ribulose-1-phosphate (MMDBc0030182)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:57:21 UTC
Update Date2022-08-31 17:40:29 UTC
Metabolite IDMMDBc0030182
Metabolite Identification
Common NameD-Ribulose-1-phosphate
DescriptionD-ribulose-1-phosphate is a pentose phosphate. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f12414740f0>

Structure #1
  Mrv0541 02241207302D          

 14 13  0  0  0  0            999 V2000
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8743    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7474    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1599   -0.3020    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  6  1  0  0  0  0
  2  4  1  0  0  0  0
  2 13  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f12414740f0>

HMDB0260227
     RDKit          3D
[(3R)-3,4,5-Trihydroxy-2-oxopentyl] dihydrogen phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
    0.2123   -1.7489    1.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0307   -0.8559    0.2973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4008   -0.3480    0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3068   -0.9953    1.0006 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8231   -0.2954    0.7283 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.8605   -1.3761    0.9308 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8644    0.1813   -0.8953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1258    0.9929    1.7632 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0575   -0.2798   -0.5158 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5721    0.7202   -1.3286 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2135    0.2168    0.3189 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7043   -0.7793    1.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3022    0.6476   -0.6721 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4183    1.1279   -0.0056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8063   -0.4667   -0.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4928    0.7395    0.3933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0361   -0.5807   -1.4910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6476    1.6910    1.2814 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4222   -1.0997   -1.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1847    1.4817   -0.8670 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9110    1.0717    0.9276 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9991   -1.5776    0.6445 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5328   -0.2244   -1.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8283    1.4161   -1.3136 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0365    0.3413    0.1011 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  5  8  1  0
  2  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  3 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
M  END
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3D SDF for #<Metabolite:0x00007f12414740f0>

Structure #1
  Mrv0541 02241207302D          

 14 13  0  0  0  0            999 V2000
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8743    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7474    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1599   -0.3020    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  6  1  0  0  0  0
  2  4  1  0  0  0  0
  2 13  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030182

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)

> <INCHI_KEY>
NBOCCPQHBPGYCX-UHFFFAOYSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.070378526223664

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3,4,5-trihydroxy-2-oxopentyl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.80

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.208722028772268

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1786190642675627

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9797461037901494

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.4722

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3,4,5-trihydroxy-2-oxopentyl)oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f12414740f0>

HMDB0260227
     RDKit          3D
[(3R)-3,4,5-Trihydroxy-2-oxopentyl] dihydrogen phosphate
 25 24  0  0  0  0  0  0  0  0999 V2000
    0.2123   -1.7489    1.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0307   -0.8559    0.2973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4008   -0.3480    0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3068   -0.9953    1.0006 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8231   -0.2954    0.7283 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.8605   -1.3761    0.9308 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8644    0.1813   -0.8953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1258    0.9929    1.7632 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0575   -0.2798   -0.5158 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5721    0.7202   -1.3286 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2135    0.2168    0.3189 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7043   -0.7793    1.1350 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3022    0.6476   -0.6721 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4183    1.1279   -0.0056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8063   -0.4667   -0.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4928    0.7395    0.3933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0361   -0.5807   -1.4910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6476    1.6910    1.2814 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4222   -1.0997   -1.1888 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1847    1.4817   -0.8670 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9110    1.0717    0.9276 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9991   -1.5776    0.6445 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5328   -0.2244   -1.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8283    1.4161   -1.3136 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0365    0.3413    0.1011 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  5  8  1  0
  2  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  3 15  1  0
  3 16  1  0
  7 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 13 23  1  0
 13 24  1  0
 14 25  1  0
M  END
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PDB for #<Metabolite:0x00007f12414740f0>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.104  -0.564   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.231  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.897  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.437  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.770  -2.874   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.897  -2.874   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.564   0.976   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       7.232   0.206   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.668  -1.897   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.128   0.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.565  -1.334   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       5.898  -0.564   0.000  0.00  0.00           P+0
CONECT    1    3    6                                                       
CONECT    2    4   13                                                       
CONECT    3    1    5    7                                                  
CONECT    4    2    5    8                                                  
CONECT    5    3    4    9                                                  
CONECT    6    1                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10   14                                                            
CONECT   11   14                                                            
CONECT   12   14                                                            
CONECT   13    2   14                                                       
CONECT   14   10   11   12   13                                             
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for #<Metabolite:0x00007f12414740f0>

COMPND    HMDB0260227
HETATM    1  O1  UNL     1       0.212  -1.749   1.071  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.031  -0.856   0.297  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.401  -0.348   0.168  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.307  -0.995   1.001  1.00  0.00           O  
HETATM    5  P1  UNL     1      -3.823  -0.295   0.728  1.00  0.00           P  
HETATM    6  O3  UNL     1      -4.861  -1.376   0.931  1.00  0.00           O  
HETATM    7  O4  UNL     1      -3.864   0.181  -0.895  1.00  0.00           O  
HETATM    8  O5  UNL     1      -4.126   0.993   1.763  1.00  0.00           O  
HETATM    9  C3  UNL     1       1.057  -0.280  -0.516  1.00  0.00           C  
HETATM   10  O6  UNL     1       0.572   0.720  -1.329  1.00  0.00           O  
HETATM   11  C4  UNL     1       2.214   0.217   0.319  1.00  0.00           C  
HETATM   12  O7  UNL     1       2.704  -0.779   1.135  1.00  0.00           O  
HETATM   13  C5  UNL     1       3.302   0.648  -0.672  1.00  0.00           C  
HETATM   14  O8  UNL     1       4.418   1.128  -0.006  1.00  0.00           O  
HETATM   15  H1  UNL     1      -1.806  -0.467  -0.873  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.493   0.740   0.393  1.00  0.00           H  
HETATM   17  H3  UNL     1      -4.036  -0.581  -1.491  1.00  0.00           H  
HETATM   18  H4  UNL     1      -4.648   1.691   1.281  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.422  -1.100  -1.189  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.185   1.482  -0.867  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.911   1.072   0.928  1.00  0.00           H  
HETATM   22  H8  UNL     1       2.999  -1.578   0.644  1.00  0.00           H  
HETATM   23  H9  UNL     1       3.533  -0.224  -1.317  1.00  0.00           H  
HETATM   24  H10 UNL     1       2.828   1.416  -1.314  1.00  0.00           H  
HETATM   25  H11 UNL     1       5.037   0.341   0.101  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4   15   16
CONECT    4    5
CONECT    5    6    6    7    8
CONECT    7   17
CONECT    8   18
CONECT    9   10   11   19
CONECT   10   20
CONECT   11   12   13   21
CONECT   12   22
CONECT   13   14   23   24
CONECT   14   25
END
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SMILES for #<Metabolite:0x00007f12414740f0>

OCC(O)C(O)C(=O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007f12414740f0>

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)
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Synonyms
ValueSource
D-Ribulose-1-phosphoric acidGenerator
Molecular FormulaC5H11O8P
Average Mass230.1098
Monoisotopic Mass230.01915384
IUPAC Name[(3,4,5-trihydroxy-2-oxopentyl)oxy]phosphonic acid
Traditional Name(3,4,5-trihydroxy-2-oxopentyl)oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(=O)COP(O)(O)=O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)
InChI KeyNBOCCPQHBPGYCX-UHFFFAOYSA-N