P. aeruginosa Metabolome Database: D-Ribulose 5-phosphate (PAMDB000638)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000638

Identification

Name:

D-Ribulose 5-phosphate

Description:

D-Ribulose 5-phosphate is a metabolite in the Pentose phosphate pathway. It is also involved in pentose and glucuronate interconversions, and in Riboflavin metabolism (KEGG)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

a-D-Ribose 5-phosphate
a-D-Ribose 5-phosphoric acid
Alpha-D-Ribose 5-phosphate
alpha-D-Ribose 5-phosphoric acid
D-Ribulose 5-phosphate
D-Ribulose 5-phosphoric acid
D-Ribulose-5-P
Erythro-Pentulose 5-phosphate
erythro-Pentulose 5-phosphoric acid
Ribulose 5-phosphate
Ribulose 5-phosphoric acid
Ribulose phosphate
Ribulose phosphoric acid
Ribulose-5-P
Ribulose-5P
Ru5P
α-D-Ribose 5-phosphate
α-D-Ribose 5-phosphoric acid

Chemical Formula:

C₅H₁₁O₈P

Average Molecular Weight:

230.1098

Monoisotopic Molecular Weight:

230.01915384

InChI Key:

FNZLKVNUWIIPSJ-UHNVWZDZSA-N

InChI:

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1

CAS number:

4151-19-3

IUPAC Name:

{[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid

Traditional IUPAC Name:

Ara

SMILES:

OCC(=O)[C@H](O)[C@H](O)COP(O)(O)=O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organooxygen compounds

Class

Carbohydrates and carbohydrate conjugates

Sub Class

Monosaccharides

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
Beta-hydroxy ketone
Beta-ketoaldehyde
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Polyol
Ketone
1,2-diol
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose 5-phosphate (CHEBI:17363 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	26.1 mg/mL	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.47 m³·mol^-1	ChemAxon
Polarizability	17.86 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

D-Ribulose 5-phosphate > 1-Deoxy-L-glycero-tetrulose 4-phosphate + Formic acid + Hydrogen ion

More...

Pathways:

Carbon fixation in photosynthetic organisms pae00710
Fructose and mannose metabolism pae00051
Glutathione metabolism pae00480
Lipopolysaccharide biosynthesis pae00540
Metabolic pathways pae01100
Microbial metabolism in diverse environments pae01120
Pentose and glucuronate interconversions pae00040
Pentose phosphate pathway pae00030
Purine metabolism pae00230
Riboflavin metabolism pae00740

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)	splash10-0a4i-2936000000-adde71232cd79c7c92aa	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)	splash10-0a4i-2947000000-ae4da5853e1b24392d1d	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-6f5913e9948fa7667e41	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-3724bb9f611bbdc1fe11	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-c36fdbcc1d3b19b2fafd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-b67b8ea484aa4ddb40e3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-82b17cf4f5a8c927fe64	View in MoNA

References

References:

Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882

Synthesis Reference:

Wong, Chi-Huey; McCurry, Stephen D.; Whitesides, George M. Practical enzymic syntheses of ribulose 1,5 bisphosphate and ribose 5-phosphate. Journal of the American Chemical Society (1980), 102(27), 7938-9.

Material Safety Data Sheet (MSDS)

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Links

External Links:

Resource	Link
CHEBI ID	17797
HMDB ID	HMDB00618
Pubchem Compound ID	439167
Kegg ID	C00199
ChemSpider ID	388327
Wikipedia	Ribulose 5-phosphate
BioCyc ID	RIBULOSE-5P
EcoCyc ID	RIBULOSE-5P
Ligand Expo	5RP

Enzymes

Protein Details

• 3,4-dihydroxy-2-butanone 4-phosphate synthase

General function:: Involved in 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
Specific function:: Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
Gene Name:: ribB
Locus Tag:: PA4054
Molecular weight:: 39.4 kDa

Reactions

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.

Protein Details

• Ribose-5-phosphate isomerase A

General function:: Involved in ribose-5-phosphate isomerase activity
Specific function:: D-ribose 5-phosphate = D-ribulose 5-phosphate
Gene Name:: rpiA
Locus Tag:: PA0330
Molecular weight:: 23.7 kDa

Reactions

D-ribose 5-phosphate = D-ribulose 5-phosphate.

Protein Details

• Ribulose-phosphate 3-epimerase

General function:: Involved in catalytic activity
Specific function:: D-ribulose 5-phosphate = D-xylulose 5- phosphate
Gene Name:: rpe
Locus Tag:: PA0607
Molecular weight:: 24.1 kDa

Reactions

D-ribulose 5-phosphate = D-xylulose 5-phosphate.

Protein Details

• Arabinose 5-phosphate isomerase

General function:: Involved in protein binding
Specific function:: Catalyzes the interconversion of D-arabinose 5-phosphate and D-ribulose 5-phosphate
Gene Name:: kdsD
Locus Tag:: PA4457
Molecular weight:: 34.2 kDa

Reactions

D-arabinose 5-phosphate = D-ribulose 5-phosphate.

D-Ribulose 5-phosphate (PAMDB000638)

Structure for D-Ribulose 5-phosphate (PAMDB000638)

Enzymes

Reactions

Reactions

Reactions

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