MiMeDB: Showing metabocard for D-Ribose-5-phosphate (MMDBc0029678)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:37:12 UTC

Update Date

2022-08-31 17:11:50 UTC

Metabolite ID

MMDBc0029678

Metabolite Identification

Common Name

D-Ribose-5-phosphate

Description

D-ribose-5-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribose 5-phosphate is both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose-5-phosphate. Ribulose-5-phosphate can reversibly isomerize to ribose-5-phosphate. Ribulose-5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentoses phosphates as well as fructose 6-phosphate and glyceraldehyde-3-phosphate (both intermediates in glycolysis). The enzyme ribose-phosphate diphosphokinase converts ribose-5-phosphate into phosphoribosyl pyrophosphate. (WikiPedia)‚Üµ

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305271900072D          

 14 14  0  0  1  0            999 V2000
   13.5797   -6.6905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3643   -6.9453    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6193   -7.7300    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.4443   -7.7300    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.6992   -6.9453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1344   -8.3974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9292   -8.3974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4838   -6.6904    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3686   -6.4131    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8785   -4.8439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8390   -5.3736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4082   -5.8834    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0318   -6.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6236   -5.6285    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  1 12  1  0  0  0  0
  2  3  1  0  0  0  0
  2 13  1  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  6  0  0  0
  4  5  1  0  0  0  0
  4  7  1  6  0  0  0
  5  8  1  0  0  0  0
  5 13  1  0  0  0  0
  9 14  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  2  0  0  0  0
 12 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029678

> <DATABASE_NAME>
MIME

> <SMILES>
OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <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)/t2-,3-,4-,5?/m1/s1

> <INCHI_KEY>
KTVPXOYAKDPRHY-SOOFDHNKSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.206703837112247

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.07

> <JCHEM_LOGP>
-2.425770307333333

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.248502666590342

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2226866612133929

> <JCHEM_PKA_STRONGEST_BASIC>
-3.680084519580305

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
40.8338

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.36e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ribofuranose 5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      25.349 -12.489   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.813 -12.965   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.289 -14.429   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.829 -14.429   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.305 -12.965   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      26.384 -15.675   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      29.735 -15.675   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      30.770 -12.489   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      23.088 -11.971   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      24.040  -9.042   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      22.099 -10.031   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      25.029 -10.982   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      28.059 -12.059   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      23.564 -10.507   0.000  0.00  0.00           P+0
CONECT    1    2   12                                                       
CONECT    2    1    3   13                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    8   13                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   14                                                            
CONECT   10   14                                                            
CONECT   11   14                                                            
CONECT   12    1   14                                                       
CONECT   13    2    5                                                       
CONECT   14    9   10   11   12                                             
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
D-Ribose 5'-phosphate	ChEBI
D-Ribose-5-p	ChEBI
Ribose 5-phosphate	ChEBI
D-Ribose 5'-phosphoric acid	Generator
Ribose 5-phosphoric acid	Generator
D-Ribose 5-phosphoric acid	Generator
D-Ribose-5-phosphate	HMDB
D-Ribose-5-phosphorate	HMDB
D-Ribose-5-phosphoric acid	HMDB
Ribose-5-p	HMDB
Ribose-5-phosphate	HMDB
Ribose-5-phosphorate	HMDB
Ribose-5-phosphoric acid	HMDB
Ribose-5P	HMDB
Ribose-5-phosphoric acid, (D-ribose)-isomer	HMDB
Ribose phosphate	HMDB
Ribose-5-phosphoric acid, (D-ribofuranose)-isomer	HMDB
Ribose 5-monophosphate	HMDB

Molecular Formula

C₅H₁₁O₈P

Average Mass

230.1098

Monoisotopic Mass

230.01915384

IUPAC Name

{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

D-ribofuranose 5-phosphate

CAS Registry Number

4151-19-3

SMILES

OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

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)/t2-,3-,4-,5?/m1/s1

InChI Key

KTVPXOYAKDPRHY-SOOFDHNKSA-N

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
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
1,2-diol
Secondary alcohol
Hemiacetal
Polyol
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribose 5-phosphate (CHEBI:52742 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	33.6 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.4	ChemAxon
logS	-0.84	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	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	40.83 m³·mol⁻¹	ChemAxon
Polarizability	18.21 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

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0024742	2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine	D-Ribose-5-phosphate	N-glycosidase Npun_R5314	Synthesis	RHEA	34755880

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	11	Human ; Human feces; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Chicken ; Cattle ; River trout ; Lion	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	123	Human feces; Human ; Human sputum; Human pleural fluid plaque; Human dental plaque; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	442	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Human saliva; Catfish	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	335	Human ; Human feces; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Chicken ; Cattle ; River trout ; Lion	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	13	Human feces; Human ; Human sputum; Human pleural fluid plaque; Human dental plaque; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	116	Human feces; Human appendix biopsy; Human ; Human stool; Human gastric fluid; Human urine; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	4	Human feces; Pig	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	28	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Human saliva; Catfish	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	10	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	14		Metabolic reconstruction
Viruses	nah	1
Eukaryota/Fungi	Ascomycota	5	Human feces; Human saliva; Human supragingival plaque	Unknown
Archaea/Archaea	Crenarchaeota	4		Metabolic reconstruction
Bacteria/Eubacteria	Aquificae	1
Bacteria/Eubacteria	Chlorobi	1
Bacteria/Eubacteria	Deinococcus-thermus	2
Bacteria/Eubacteria	Cyanobacteria	8
Bacteria	nah	1
Bacteria/Eubacteria	Thermotogae	9
Bacteria/Eubacteria	Chloroflexi	3
Bacteria/Eubacteria	Gemmatimonadetes	1
Bacteria/Eubacteria	Acidobacteria	1
Bacteria/Eubacteria	Dictyoglomi	2
Bacteria/Eubacteria	Elusimicrobia	1
Viruses/Bamfordvirae	Nucleocytoviricota	1

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001548

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

52742

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wohlhueter RM, McIvor RS, Plagemann PG: Facilitated transport of uracil and 5-fluorouracil, and permeation of orotic acid into cultured mammalian cells. J Cell Physiol. 1980 Sep;104(3):309-19. doi: 10.1002/jcp.1041040305. [PubMed:7419607 ]
Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for D-Ribose-5-phosphate (MMDBc0029678)

MOL for #<Metabolite:0x00005645c9ed0cc8>

3D MOL for #<Metabolite:0x00005645c9ed0cc8>

3D SDF for #<Metabolite:0x00005645c9ed0cc8>

3D-SDF for #<Metabolite:0x00005645c9ed0cc8>

PDB for #<Metabolite:0x00005645c9ed0cc8>

3D PDB for #<Metabolite:0x00005645c9ed0cc8>

SMILES for #<Metabolite:0x00005645c9ed0cc8>

INCHI for #<Metabolite:0x00005645c9ed0cc8>

Structure for #<Metabolite:0x00005645c9ed0cc8>

3D Structure for #<Metabolite:0x00005645c9ed0cc8>