MiMeDB: Showing metabocard for D-ribofuranose 5-phosphate (MMDBc0032135)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:03:49 UTC

Update Date

2022-08-31 18:30:48 UTC

Metabolite ID

MMDBc0032135

Metabolite Identification

Common Name

D-ribofuranose 5-phosphate

Description

D-ribofuranose 5-phosphate is an intermediate in several pathways in E. coli., adenosine nucleotides degradation III, NAD salvage pathway I and D-ribofuranose 5-phosphate pathway. In adenosine nucleotides degradation III pathway, it is a product for enzyme AMP nucleosidase which catalyzes the reaction AMP + H2O -> D-ribofuranose 5-phosphate + adenine. It is also a product for enzyme NMN nucleosidase that catalyzes the reaction beta-nicotinamide D-ribonucleotide + H2O -> D-ribofuranose 5-phosphate + nicotinamide + H+ in pathway NAD salvage pathway I. It is a substrate for enzyme pseudouridine 5'-phosphate glycosidase that catalyzes the reaction D-ribofuranose 5-phosphate + uracil -> pseudouridine 5'-phosphate + H2O in pseudouridine degradation pathway (BioCyc compound: CPD-15317).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 03311515082D          

 14 14  0  0  0  0            999 V2000
   -0.7366    0.2999    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4040   -0.1850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1491   -0.9696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3241   -0.9696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0692   -0.1850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6340   -1.6370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1608   -1.6370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7154    0.0698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1886    0.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8017   -0.1696    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5863   -0.2272    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3556   -0.1766    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.6016    0.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5933   -1.1011    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  2  9  1  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  5  8  1  0  0  0  0
  4  7  1  0  0  0  0
  3  6  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 14  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  CHG  2  12  -1  14  -1
M  END
> <DATABASE_ID>
MMDBc0032135

> <DATABASE_NAME>
MIME

> <SMILES>
OC1OC(COP([O-])([O-])=O)C(O)C1O

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

> <INCHI_KEY>
KTVPXOYAKDPRHY-UHFFFAOYSA-L

> <FORMULA>
C5H9O8P

> <MOLECULAR_WEIGHT>
228.094

> <EXACT_MASS>
228.004601408

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.706249828411643

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3,4,5-trihydroxyoxolan-2-yl)methyl phosphate

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-2.425770307333333

> <ALOGPS_LOGS>
-0.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.248502666590346

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2226866612133929

> <JCHEM_PKA_STRONGEST_BASIC>
-3.680084519580305

> <JCHEM_POLAR_SURFACE_AREA>
142.34

> <JCHEM_REFRACTIVITY>
38.5904

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.15e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3,4,5-trihydroxyoxolan-2-yl)methyl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 31-MAR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAR-15         0                                  
HETATM    1  O   UNK     0      -1.375   0.560   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.621  -0.345   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.145  -1.810   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.605  -1.810   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.129  -0.345   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.050  -3.056   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.300  -3.056   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.335   0.130   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -4.085   0.130   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.230  -0.317   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      -6.694  -0.424   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      -8.130  -0.330   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0      -6.723   1.290   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -6.707  -2.055   0.000  0.00  0.00           O-1
CONECT    1    2    5                                                       
CONECT    2    3    9    1                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    1    8                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    2   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   14   12   13                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
D-Ribofuranose 5-phosphoric acid ⇥	Generator

Molecular Formula

C₅H₉O₈P

Average Mass

228.094

Monoisotopic Mass

228.004601408

IUPAC Name

(3,4,5-trihydroxyoxolan-2-yl)methyl phosphate

Traditional Name

(3,4,5-trihydroxyoxolan-2-yl)methyl phosphate

CAS Registry Number

Not Available

SMILES

OC1OC(COP([O-])([O-])=O)C(O)C1O

InChI Identifier

InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/p-2

InChI Key

KTVPXOYAKDPRHY-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Oxolane
Secondary alcohol
1,2-diol
Hemiacetal
Polyol
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

a pentose-5-phosphate (RIBOSE-5P )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	91.5 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.4	ChemAxon
logS	-0.46	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	142.34 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	38.59 m³·mol⁻¹	ChemAxon
Polarizability	17.71 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

4357561

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for D-ribofuranose 5-phosphate (MMDBc0032135)

MOL for #<Metabolite:0x0000560be1b06740>

3D MOL for #<Metabolite:0x0000560be1b06740>

3D SDF for #<Metabolite:0x0000560be1b06740>

3D-SDF for #<Metabolite:0x0000560be1b06740>

PDB for #<Metabolite:0x0000560be1b06740>

3D PDB for #<Metabolite:0x0000560be1b06740>

SMILES for #<Metabolite:0x0000560be1b06740>

INCHI for #<Metabolite:0x0000560be1b06740>

Structure for #<Metabolite:0x0000560be1b06740>

3D Structure for #<Metabolite:0x0000560be1b06740>