MiMeDB: Showing metabocard for alpha-D-ribose 5-phosphate (MMDBc0033082)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:33:59 UTC

Update Date

2025-01-15 22:29:25 UTC

Metabolite ID

MMDBc0033082

Metabolite Identification

Common Name

alpha-D-ribose 5-phosphate

Description

D-Arabinose 5-phosphate is an intermediate in biosynthesis of lipopolysaccharide. It is reversibly converted to D-ribulose 5-phosphate by arabinose-5-phosphate isomerase (EC 5.3.1.13).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₅H₁₁O₈P

Average Mass

230.1098

Monoisotopic Mass

230.0191538

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

4300-28-1

SMILES

Not Available

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-AIHAYLRMSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Not Available

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (retained)	2025-10-24	543.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	423.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	43.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	232.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	298.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	305.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	451.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	816.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	825.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	178.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	419.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	190.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	27.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	448.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	807.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	78.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	319.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	639.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	562.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_1	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O	standard non polar	2025-10-24	1715.12
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_2	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H](O)[C@@H]1O	standard non polar	2025-10-24	1821.45
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_3	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@H]1O	standard non polar	2025-10-24	2154.21
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_4	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O	standard non polar	2025-10-24	1545.67
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_5	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-24	2162.78
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_6	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2192.53
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_7	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O)[C@H]1O	standard non polar	2025-10-24	1670.45
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_8	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2626.26
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_9	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@H](O)[C@@H]1O	standard non polar	2025-10-24	1822.91
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_10	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-24	1967.68
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_11	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O)O[Si](C)(C)C	standard non polar	2025-10-24	2147.22
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_12	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2045.82
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_13	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-24	1611.89
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_14	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2482.14
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_15	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O	standard non polar	2025-10-24	2301.62
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_16	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1685.37
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_17	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@H](O)[C@@H]1O	standard non polar	2025-10-24	2033.82
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_18	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H]1O	standard non polar	2025-10-24	2177.09
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_19	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2223.98
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_20	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-24	2727.04
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_21	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2314.52
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_22	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1994.47
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_23	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1954.07
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_1	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O	standard polar	2025-10-24	1932.82
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_2	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H](O)[C@@H]1O	standard polar	2025-10-24	1711.39
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_3	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@H]1O	standard polar	2025-10-24	1707.22
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_4	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O	standard polar	2025-10-24	1756.46
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_5	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-24	1806.02
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_6	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2287.58
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_7	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O)[C@H]1O	standard polar	2025-10-24	2078.46
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_8	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2318.15
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_9	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@H](O)[C@@H]1O	standard polar	2025-10-24	2563.04
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_10	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-24	2078.69
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_11	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O)O[Si](C)(C)C	standard polar	2025-10-24	2268.83
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_12	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1751.68
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_13	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-24	2867.79
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_14	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2500.13
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_15	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O	standard polar	2025-10-24	2255.38
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_16	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2407.51
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_17	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@H](O)[C@@H]1O	standard polar	2025-10-24	1584.13
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_18	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H]1O	standard polar	2025-10-24	2367.92
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_19	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2668.49
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_20	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-24	2869.44
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_21	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1173.98
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_22	C[Si](C)(C)O[C@H]1[C@@H](O)O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1255.63
Gas Chromatography	alpha-D-ribose 5-phosphate_TMS_23	C[Si](C)(C)O[C@H]1O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	1751.18

Biological Properties

Cellular Locations

Cytoplasm
Mitochondria

Biospecimen Locations

Blood
Feces
Prostate
Urine

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
MMDBp0192212	Ribose-phosphate pyrophosphokinase 3	Unknown	P21108	Homo sapiens
MMDBp0192269	ADP-sugar pyrophosphatase	Unknown	Q9UKK9	Homo sapiens
MMDBp0192270	Ribose-phosphate pyrophosphokinase 1	Unknown	P60891	Homo sapiens
MMDBp0192274	Ribose-phosphate pyrophosphokinase 2	Unknown	P11908	Homo sapiens
MMDBp0192280	ADP-ribose pyrophosphatase, mitochondrial	Unknown	Q9BW91	Homo sapiens
MMDBp0192420	Transketolase-like protein 1	Unknown	P51854	Homo sapiens
MMDBp0192425	Transketolase	Unknown	P29401	Homo sapiens
MMDBp0192694	Ribokinase	Enzyme	Q9H477	Homo sapiens
MMDBp0191639	Phosphoglucomutase-1	Enzyme	P36871	Escherichia coli
MMDBp0193141	Phosphoacetylglucosamine mutase	Unknown	O95394	Homo sapiens
MMDBp0193159	Ribose-5-phosphate isomerase	Enzyme	P49247	Homo sapiens
MMDBp0193368	Transient receptor potential cation channel subfamily M member 2	Unknown	O94759	Homo sapiens
MMDBp0193931	Phosphoglucomutase-2	Unknown	Q96G03	Homo sapiens
MMDBp0194056	Transketolase-like protein 2	Unknown	Q9H0I9	Homo sapiens
MMDBp0196256	Putative uncharacterized protein PRPS2	Enzyme	A6NMS2	Homo sapiens
MMDBp0196257	Ribose-phosphate pyrophosphokinase	Enzyme	Q53FW2	Homo sapiens
MMDBp0196679	Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase	Unknown	Q3LIE5

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
MMDBr0018463	D-Ribulose 5-phosphate	alpha-D-ribose 5-phosphate	Ribose-5-phosphate isomerase A	Isomerization	PathBank	31602464
MMDBr0018464	Xylulose 5-phosphate	D-Sedoheptulose 7-phosphate	Transketolase 1	Transfer of ketol group	PathBank	31602464
MMDBr0018502	alpha-D-ribose 5-phosphate	Phosphoribosyl pyrophosphate	Ribose-phosphate pyrophosphokinase	Phosphorylation	PathBank	31602464
MMDBr0018503	alpha-D-ribose 5-phosphate	Ribose-1-phosphate	Phosphopentomutase	Transfers of a phosphate group; Isomerization; Intramolecular transfer of functional group	PathBank	31602464
MMDBr0019169	Ribose-1-phosphate	alpha-D-ribose 5-phosphate	Phosphopentomutase	Transfers of a phosphate group; Isomerization; Intramolecular transfer of functional group	PathBank	31602464
MMDBr0019331	Adenosine monophosphate	Adenine	AMP nucleosidase	Hydrolysis of a nucleotide	PathBank	31602464
MMDBr0019370	D-Ribose	alpha-D-ribose 5-phosphate	Ribokinase	Phosphorylation	PathBank	31602464
MMDBr0019572	alpha-D-ribose 5-phosphate	Phosphoribosyl pyrophosphate	Ribose-phosphate pyrophosphokinase 1	Phosphorylation	PathBank	31602464
MMDBr0019615	D-Ribulose 5-phosphate	alpha-D-ribose 5-phosphate	Ribose-5-phosphate isomerase	Isomerization	PathBank	31602464
MMDBr0019618	Xylulose 5-phosphate	D-Sedoheptulose 7-phosphate	Transketolase 1	Transfer of ketol group	PathBank	31602464
MMDBr0020054	D-Sedoheptulose 7-phosphate	Xylulose 5-phosphate	Transketolase 1	Transfer of ketol group	PathBank	31602464
MMDBr0020055	alpha-D-ribose 5-phosphate	D-Ribulose 5-phosphate	Ribose-5-phosphate isomerase	Isomerization	PathBank	31602464

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified	Children (6 - 18 years old)	Not Specified	Normal	HMDB	27609529
Human Urine	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Prostate	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597

External Links

Not Available

General References

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]

Showing metabocard for alpha-D-ribose 5-phosphate (MMDBc0033082)

MOL for #<Metabolite:0x00007f2dece10ea8>

3D MOL for #<Metabolite:0x00007f2dece10ea8>

3D SDF for #<Metabolite:0x00007f2dece10ea8>

3D-SDF for #<Metabolite:0x00007f2dece10ea8>

PDB for #<Metabolite:0x00007f2dece10ea8>

3D PDB for #<Metabolite:0x00007f2dece10ea8>

SMILES for #<Metabolite:0x00007f2dece10ea8>

INCHI for #<Metabolite:0x00007f2dece10ea8>

Structure for #<Metabolite:0x00007f2dece10ea8>

3D Structure for #<Metabolite:0x00007f2dece10ea8>