Showing metabocard for Ribose-1-phosphate (MMDBc0029808)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:42:34 UTC
Update Date2024-04-30 19:42:11 UTC
Metabolite IDMMDBc0029808
Metabolite Identification
Common NameRibose-1-phosphate
DescriptionRibose 1-phosphate is an intermediate in the metabolism of Pyrimidine and the metabolism of Nicotinate and nicotinamide. It is a substrate for Uridine phosphorylase 2, Phosphoglucomutase, Purine nucleoside phosphorylase and Uridine phosphorylase 1. Ribose 1-phosphate can be formed from guanosine through the action of purine nucleoside phosphorylase. Ribose 1-phosphate can also act as a ribose donor in the synthesis of xanthosine as catalyzed by the same enzyme (purine nucleoside phosphorylase). The presence of guanase, which irreversibly converts guanine to xanthine, affects the overall process of guanosine transformation. The activated ribose moiety in Ribose 1-phosphate which stems from the catabolism of purine nucleosides can be transferred to uracil and, in the presence of ATP, used for the synthesis of pyrimidine nucleotides; therefore, purine nucleosides can act as ribose donors for the salvage of pyrimidine bases. (PMID: 9133638 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000556b6ab77958>

439236
  Mrv0541 02231216412D          

 14 14  0  0  1  0            999 V2000
    2.6150    1.0082    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2386    0.4311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7865    0.2011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1360   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3412   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8622    1.0082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4435    1.8151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8081    0.8366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4220    1.1797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6511   -0.8384    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8261   -0.8384    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9060   -0.0538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5712   -0.0538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6907    0.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  2  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13  3  1  1  0  0  0
 10  4  1  1  0  0  0
 11  5  1  1  0  0  0
  6 14  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x0000556b6ab77958>

HMDB0001489
     RDKit          3D
Ribose 1-phosphate
 25 25  0  0  0  0  0  0  0  0999 V2000
    4.2205   -0.8532   -0.7464 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1285   -0.0959   -0.0026 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.3430    1.5794   -0.1852 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2984   -0.4797    1.6365 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6565   -0.5846   -0.6263 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    0.0600   -0.0011 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1366    0.7921   -0.9073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4824    0.6000   -0.6530 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9743    1.4316    0.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3333    1.1531    0.6688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5208   -0.8862   -0.3129 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1909   -1.5689   -1.4748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3173   -0.9562    0.6256 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2705   -2.2210    0.6044 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4649    2.0009    0.0590 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.4103    1.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0197    0.7383    0.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0885    0.8341   -1.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3915    1.2209    1.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8456    2.4942    0.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8649    1.9841    0.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4456   -1.1978    0.1565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5208   -1.0473   -1.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6473   -0.6916    1.6418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3248   -2.8961    1.0149 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13  6  1  0
  3 15  1  0
  4 16  1  0
  6 17  1  1
  8 18  1  6
  9 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  1
 12 23  1  0
 13 24  1  1
 14 25  1  0
M  END
Download

3D SDF for #<Metabolite:0x0000556b6ab77958>

439236
  Mrv0541 02231216412D          

 14 14  0  0  1  0            999 V2000
    2.6150    1.0082    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2386    0.4311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7865    0.2011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1360   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3412   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8622    1.0082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4435    1.8151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8081    0.8366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4220    1.1797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6511   -0.8384    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8261   -0.8384    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9060   -0.0538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5712   -0.0538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6907    0.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  2  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13  3  1  1  0  0  0
 10  4  1  1  0  0  0
 11  5  1  1  0  0  0
  6 14  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029808

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
YXJDFQJKERBOBM-TXICZTDVSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.165952447471312

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-2.425770307333333

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.218897432342067

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1553760127282273

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811597090040385

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
40.833800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.52e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribose 1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x0000556b6ab77958>

HMDB0001489
     RDKit          3D
Ribose 1-phosphate
 25 25  0  0  0  0  0  0  0  0999 V2000
    4.2205   -0.8532   -0.7464 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1285   -0.0959   -0.0026 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.3430    1.5794   -0.1852 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2984   -0.4797    1.6365 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6565   -0.5846   -0.6263 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5889    0.0600   -0.0011 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1366    0.7921   -0.9073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4824    0.6000   -0.6530 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9743    1.4316    0.5127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3333    1.1531    0.6688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5208   -0.8862   -0.3129 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1909   -1.5689   -1.4748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3173   -0.9562    0.6256 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2705   -2.2210    0.6044 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4649    2.0009    0.0590 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.4103    1.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0197    0.7383    0.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0885    0.8341   -1.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3915    1.2209    1.4341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8456    2.4942    0.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8649    1.9841    0.7190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4456   -1.1978    0.1565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5208   -1.0473   -1.9746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6473   -0.6916    1.6418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3248   -2.8961    1.0149 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13  6  1  0
  3 15  1  0
  4 16  1  0
  6 17  1  1
  8 18  1  6
  9 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  1
 12 23  1  0
 13 24  1  1
 14 25  1  0
M  END
Download

PDB for #<Metabolite:0x0000556b6ab77958>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 439236                                            
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0       4.881   1.882   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0       7.912   0.805   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       5.201   0.375   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.587  -2.811   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       6.237  -2.811   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      10.943   1.882   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.561   3.388   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.375   1.562   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.388   2.202   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.682  -1.565   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.142  -1.565   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.158  -0.100   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.666  -0.100   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.623   0.375   0.000  0.00  0.00           C+0
CONECT    1    3    7    8    9                                             
CONECT    2   12   13                                                       
CONECT    3    1   13                                                       
CONECT    4   10                                                            
CONECT    5   11                                                            
CONECT    6   14                                                            
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    1                                                            
CONECT   10    4   11   12                                                  
CONECT   11    5   10   13                                                  
CONECT   12    2   10   14                                                  
CONECT   13    2    3   11                                                  
CONECT   14    6   12                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END
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3D PDB for #<Metabolite:0x0000556b6ab77958>

COMPND    HMDB0001489
HETATM    1  O1  UNL     1       4.221  -0.853  -0.746  1.00  0.00           O  
HETATM    2  P1  UNL     1       3.129  -0.096  -0.003  1.00  0.00           P  
HETATM    3  O2  UNL     1       3.343   1.579  -0.185  1.00  0.00           O  
HETATM    4  O3  UNL     1       3.298  -0.480   1.637  1.00  0.00           O  
HETATM    5  O4  UNL     1       1.657  -0.585  -0.626  1.00  0.00           O  
HETATM    6  C1  UNL     1       0.589   0.060  -0.001  1.00  0.00           C  
HETATM    7  O5  UNL     1      -0.137   0.792  -0.907  1.00  0.00           O  
HETATM    8  C2  UNL     1      -1.482   0.600  -0.653  1.00  0.00           C  
HETATM    9  C3  UNL     1      -1.974   1.432   0.513  1.00  0.00           C  
HETATM   10  O6  UNL     1      -3.333   1.153   0.669  1.00  0.00           O  
HETATM   11  C4  UNL     1      -1.521  -0.886  -0.313  1.00  0.00           C  
HETATM   12  O7  UNL     1      -1.191  -1.569  -1.475  1.00  0.00           O  
HETATM   13  C5  UNL     1      -0.317  -0.956   0.626  1.00  0.00           C  
HETATM   14  O8  UNL     1       0.270  -2.221   0.604  1.00  0.00           O  
HETATM   15  H1  UNL     1       2.465   2.001   0.059  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.094  -1.410   1.829  1.00  0.00           H  
HETATM   17  H3  UNL     1       1.020   0.738   0.759  1.00  0.00           H  
HETATM   18  H4  UNL     1      -2.088   0.834  -1.532  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.391   1.221   1.434  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.846   2.494   0.226  1.00  0.00           H  
HETATM   21  H7  UNL     1      -3.865   1.984   0.719  1.00  0.00           H  
HETATM   22  H8  UNL     1      -2.446  -1.198   0.157  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.521  -1.047  -1.975  1.00  0.00           H  
HETATM   24  H10 UNL     1      -0.647  -0.692   1.642  1.00  0.00           H  
HETATM   25  H11 UNL     1      -0.325  -2.896   1.015  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    3   15
CONECT    4   16
CONECT    5    6
CONECT    6    7   13   17
CONECT    7    8
CONECT    8    9   11   18
CONECT    9   10   19   20
CONECT   10   21
CONECT   11   12   13   22
CONECT   12   23
CONECT   13   14   24
CONECT   14   25
END
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SMILES for #<Metabolite:0x0000556b6ab77958>

OC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
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INCHI for #<Metabolite:0x0000556b6ab77958>

InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
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Synonyms
ValueSource
1-O-Phosphono-alpha-D-ribofuranoseChEBI
1-Phospho-alpha-D-ribofuranoseChEBI
D-Ribose 1-phosphateChEBI
1-O-Phosphono-a-D-ribofuranoseGenerator
1-O-Phosphono-α-D-ribofuranoseGenerator
1-Phospho-a-D-ribofuranoseGenerator
1-Phospho-α-D-ribofuranoseGenerator
D-Ribose 1-phosphoric acidGenerator
Ribose 1-phosphoric acidGenerator
1-O-Phosphono-D-ribofuranoseHMDB
a-D-Ribofuranose 1-(dihydrogen phosphate)HMDB
a-D-Ribose 1-phosphateHMDB
alpha-D-Ribofuranose 1-(dihydrogen phosphate)HMDB
alpha-D-Ribofuranose 1-phosphateHMDB
alpha-D-Ribose 1-phosphateHMDB
D-Ribofuranose 1-(dihydrogen phosphate)HMDB
D-Ribofuranose 1-phosphateHMDB
D-Ribose-1-phosphateHMDB
D-Ribose-1PHMDB
Ribofuranose 1-phosphateHMDB
Ribose 1-phosphate, (beta-D)-isomerHMDB
Ribose 1-phosphate, (alpha-D)-isomerHMDB
Molecular FormulaC5H11O8P
Average Mass230.1098
Monoisotopic Mass230.01915384
IUPAC Name{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional Nameribose 1-phosphate
CAS Registry Number14075-00-4
SMILES
OC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
InChI KeyYXJDFQJKERBOBM-TXICZTDVSA-N