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

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-014j-1942000000-8c3468eabd202324a3ae	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)	splash10-00di-9532000000-693524b08b2ccd6179c5	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)	splash10-00di-9421000000-dbcd94d0a73f35716059	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1942000000-8c3468eabd202324a3ae	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9532000000-693524b08b2ccd6179c5	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9421000000-dbcd94d0a73f35716059	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9320000000-9b5fdcbd0e9ea3ece549	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-06vi-9164100000-2305f99f73e0c553d514	2017-10-06	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-9320000000-7f3d980d223a6b9f5f3f	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0002-9000000000-a5df0614f5cbd8b55405	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-056r-0090700000-ea86961dacc666b5fc7d	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-004i-0090000000-10949588537786dbae1e	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-002b-9000000000-49264a7584727750bd70	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-004i-0090000000-10949588537786dbae1e	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-002b-9000000000-340deaecb0169ce2acd3	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-1790000000-a3ced14cd6c2537c6d8f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-5940000000-8bcb763477232ce1dd2c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00y1-9300000000-ff5bd2489969fca00eb7	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-7190000000-184075252146923d2684	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-917b1eb059131caa49ac	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-579393c266ea056c9e74	2016-09-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY 2D NMR Spectrum (experimental)		2012-12-04	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0000231	Adenosine diphosphate ribose	Adenosine monophosphate	Nudix hydrolase 9	ADPribose Diphosphatase, Mitochondrial	VMH	12427752 12948489 15347676
MMDBr0002496	D-Ribose-5-phosphate	D-Ribulose 5-phosphate	Ribose 5-phosphate isomerase a	D-Ribose-5-Phosphate Ketol-Isomerase	VMH	14690456 14988808 15234337 2843500
MMDBr0002741	D-Ribose-5-phosphate	D-Ribose-5-phosphate	Not Available	Free Diffusion	VMH	7419607
MMDBr0007055	Cytidine monophosphate	Cytosine	Not Available	CMP nucleosidase	VMH	30371894
MMDBr0007539	Ribose-1-phosphate	D-Ribose-5-phosphate	Not Available	Phosphopentomutase	VMH	30371894
MMDBr0007547	Adenosine triphosphate	Adenosine monophosphate	Not Available	Phosphoribosylpyrophosphate Synthetase	VMH	30371894
MMDBr0007564	D-Ribose-5-phosphate	D-Ribulose 5-phosphate	Not Available	Ribose-5-Phosphate Isomerase	VMH	30371894
MMDBr0007578	D-Ribose-5-phosphate	Glyceraldehyde 3-phosphate	Not Available	Transketolase	VMH	30371894
MMDBr0007653	Adenosine diphosphate ribose	Adenosine monophosphate	Not Available	ADPribose Diphosphatase	VMH	30371894
MMDBr0007667	Adenosine triphosphate	ADP	Not Available	Ribokinase	VMH	30371894
MMDBr0007719	Adenosine monophosphate	Adenine	Not Available	AMP nucleosidase	VMH	30371894
MMDBr0008122	Water	Hydrogen Ion	Not Available	NMN transport via NMN glycohydrolase	VMH	30371894
MMDBr0010593	Water	D-Ribose-5-phosphate	Rna pseudouridylate synthase domain containing 4	Uracil Hydro-Lyase (Adding D-Ribose 5-Phosphate;Pseudouridine-5'-Phosphate-Forming)	VMH	30371894
MMDBr0012900	ADP-D-ribose	Adenosine monophosphate	ADP-ribose pyrophosphatase	Dephosphorylation; Hydrolysis of bond	RHEA	34755880
MMDBr0012901	ADP-D-ribose	Adenosine monophosphate	ADP-ribose pyrophosphatase	Dephosphorylation	RHEA	34755880
MMDBr0013244	Adenosine triphosphate	ADP	Ribokinase	Phosphorylation	RHEA	34755880
MMDBr0013444	Adenosine triphosphate	Phosphoribosyl pyrophosphate	Ribose-phosphate pyrophosphokinase 1	Phosphorylation	RHEA	34755880
MMDBr0013755	D-Ribose-5-phosphate	Water	Pseudouridine-5'-phosphate glycosidase	Transfer of a glycosyl group	RHEA	34755880
MMDBr0013809	Ribose-1-phosphate	D-Ribose-5-phosphate	Phosphopentomutase	Transfers of a phosphate group; Isomerization; Intramolecular transfer of functional group	RHEA	34755880
MMDBr0013961	Adenosine monophosphate	Adenine	AMP nucleosidase	Hydrolysis of bond	RHEA	34755880
MMDBr0013995	Water	D-Ribose-5-phosphate	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	Hydrolysis of a nucleotide	RHEA	34755880
MMDBr0014960	CMP	Cytosine	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	Hydrolysis of a nucleotide	RHEA	34755880
MMDBr0015808	D-ribose 2,5-bisphosphate	D-Ribose-5-phosphate	Phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	RHEA	34755880
MMDBr0016392	Water	D-Ribose-5-phosphate	Bifunctional cytokinin biosynthesis protein	Hydrolysis of bond; Synthesis	RHEA	34755880
MMDBr0016393	9-ribosyl-trans-zeatin 5'-phosphate	D-Ribose-5-phosphate	Bifunctional cytokinin biosynthesis protein	Hydrolysis of bond; Synthesis	RHEA	34755880
MMDBr0016625	Water	D-Ribose-5-phosphate	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	Hydrolysis of a nucleotide	RHEA	34755880
MMDBr0016626	GMP	D-Ribose-5-phosphate	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	Hydrolysis of a nucleotide	RHEA	34755880
MMDBr0016770	5-amino-6-(5-phospho-D-ribosylamino)uracil	5,6-diaminouracil	N-glycosidase YbiA	Synthesis	RHEA	34755880
MMDBr0024742	Water	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	345	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	136	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	Firmicutes	469	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Human saliva; Catfish	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	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	3	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	4	Human feces; Pig	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Tenericutes	10	Human feces; Human	Metabolic reconstruction
Bacteria	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	Aquificae	1
Bacteria	Chlorobi	1
Bacteria	Deinococcus-thermus	2
Bacteria	Cyanobacteria	8
Bacteria/NULL	Firmicutes	1	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Human saliva; Catfish	Metabolic reconstruction
Bacteria	nah	1
Bacteria	Thermotogae	9
Bacteria	Chloroflexi	3
Bacteria	Gemmatimonadetes	1
Bacteria	Acidobacteria	1
Bacteria	Dictyoglomi	2
Bacteria	Elusimicrobia	1
Bacteria/NULL	Proteobacteria	1	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
Viruses/Bamfordvirae	Nucleocytoviricota	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Animal	Milk	Bos taurus	FooDB	31437929
Animal	Milk	Bos taurus	FooDB	31437929

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:0x00007f5a603117f0>

3D MOL for #<Metabolite:0x00007f5a603117f0>

3D SDF for #<Metabolite:0x00007f5a603117f0>

3D-SDF for #<Metabolite:0x00007f5a603117f0>

PDB for #<Metabolite:0x00007f5a603117f0>

3D PDB for #<Metabolite:0x00007f5a603117f0>

SMILES for #<Metabolite:0x00007f5a603117f0>

INCHI for #<Metabolite:0x00007f5a603117f0>

Structure for #<Metabolite:0x00007f5a603117f0>

3D Structure for #<Metabolite:0x00007f5a603117f0>