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Record Information

Version

2.0

Creation Date

2012-05-31 14:06:36 -0600

Update Date

2015-09-13 12:56:14 -0600

Secondary Accession Numbers

ECMDB04148

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

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

Weight:

Average: 230.1098
Monoisotopic: 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

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
Acyloin
Beta-hydroxy ketone
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Primary 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 g/L	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	17.95 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 <>3 3,4-Dihydroxy-2-butanone-4-P + Formic acid
D-Arabinose 5-phosphate <> D-Ribulose 5-phosphate
D-Ribose-5-phosphate <> D-Ribulose 5-phosphate
D-Ribulose 5-phosphate <>3 3,4-Dihydroxy-2-butanone-4-P + Formic acid + Hydrogen ion
D-Arabinose 5-phosphate <> D-Ribulose 5-phosphate

More...

SMPDB Pathways:

Flavin biosynthesis	PW001971
Glutathione metabolism	PW000833
Lipopolysaccharide biosynthesis	PW000831
Pentose Phosphate	PW000893
ketogluconate metabolism	PW002003
lipopolysaccharide biosynthesis II	PW001905
lipopolysaccharide biosynthesis III	PW002059

KEGG Pathways:

Carbon fixation in photosynthetic organisms ec00710
Fructose and mannose metabolism ec00051
Glutathione metabolism ec00480
Lipopolysaccharide biosynthesis ec00540
Metabolic pathways eco01100
Microbial metabolism in diverse environments ec01120
Pentose and glucuronate interconversions ec00040
Pentose phosphate pathway ec00030
Purine metabolism ec00230
Riboflavin metabolism ec00740

EcoCyc Pathways:

CMP-KDO biosynthesis I PWY-1269
flavin biosynthesis I (bacteria and plants) RIBOSYN2-PWY
pentose phosphate pathway (non-oxidative branch) NONOXIPENT-PWY
pentose phosphate pathway (oxidative branch) OXIDATIVEPENT-PWY

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
78± 0 uM	BW25113	48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L Gluco	Stationary Phase, glucose limited	Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h	37 oC	PMID: 17379776
1020± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerol	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
686± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetate	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
1320± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621

Find out more about how we convert literature concentrations.

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-EI-TOF (Non-derivatized)	splash10-0a4j-1935000000-dfb75754c9a7045f108f	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4j-1935000000-31be2cabeeebc480c1b8	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pba-1924000000-11aca642135096a8e378	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1943000000-34588179b9bd7796e907	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pbj-2914000000-d91b422c677fd9231297	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0592-9800000000-d336b0e2eff1402939d8	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-029t-9327100000-10a5d90f15e25f16925c	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004j-9010000000-49c14e85e3a3dee61721	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 10V, positive	splash10-00ec-0970000000-6e833fd34cda3327e6ae	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 15V, positive	splash10-007o-0930000000-72bf0b63618d4b200421	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 17V, positive	splash10-007o-0920000000-fe7037f21876801587ec	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 20V, positive	splash10-007o-0910000000-5dacb5e16b8a32f079c0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 23V, positive	splash10-007o-0900000000-1d35981b82e13d258d9d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 25V, positive	splash10-00ec-0900000000-23938808d1a77a77203d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 27V, positive	splash10-00dl-0900000000-abc2b8be05c39eef69e6	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, positive	splash10-00di-0190000000-f09b49c51cfa01814ef3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, positive	splash10-00di-0490000000-acd1f6a33bd147e29ac3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-00ec-0980000000-e8070ccdca137f841520	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-007o-0940000000-0e8aaff469756dafc2ee	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 8V, positive	splash10-000x-0920000000-bef5b5a1a6528a057748	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 9V, positive	splash10-000x-0910000000-7a57ccc066185b618224	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 11V, positive	splash10-007o-0900000000-0412a8fa5b22fb04ec87	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-007o-0900000000-e655723668ec0397d76e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, positive	splash10-00dl-0900000000-4d7aa68ec0ea7a05fe8b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, positive	splash10-00di-1900000000-ef58c4a909999b72f8fa	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 22V, positive	splash10-0229-4900000000-6c4c40d2771cf3aec25f	View in MoNA
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
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

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)

Download (PDF)

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

1. 6-phosphogluconate dehydrogenase, decarboxylating

General function:: Involved in oxidation-reduction process
Specific function:: Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
Gene Name:: gnd
Uniprot ID:: P00350
Molecular weight:: 51481

Reactions

6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH.

Protein Details

2. Ribulokinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + L(or D)-ribulose = ADP + L(or D)- ribulose 5-phosphate
Gene Name:: araB
Uniprot ID:: P08204
Molecular weight:: 61089

Reactions

ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.

Protein Details

3. 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
Uniprot ID:: P0A7J0
Molecular weight:: 23353

Reactions

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

Protein Details

4. 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
Uniprot ID:: P0A7Z0
Molecular weight:: 22860

Reactions

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

Protein Details

5. Probable phosphoribulokinase

General function:: Involved in ATP binding
Specific function:: ATP + D-ribulose 5-phosphate = ADP + D- ribulose 1,5-bisphosphate
Gene Name:: prkB
Uniprot ID:: P0AEX5
Molecular weight:: 32344

Reactions

ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate.

Protein Details

6. Ribulose-phosphate 3-epimerase

General function:: Involved in catalytic activity
Specific function:: D-ribulose 5-phosphate = D-xylulose 5- phosphate
Gene Name:: rpe
Uniprot ID:: P0AG07
Molecular weight:: 24554

Reactions

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

Protein Details

7. Ribose-5-phosphate isomerase B

General function:: Involved in carbohydrate metabolic process
Specific function:: In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate
Gene Name:: rpiB
Uniprot ID:: P37351
Molecular weight:: 16073

Reactions

D-ribose 5-phosphate = D-ribulose 5-phosphate.
D-allose 6-phosphate = D-allulose 6-phosphate.

Protein Details

8. 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
Uniprot ID:: P45395
Molecular weight:: 35196

Reactions

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

Protein Details

9. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

General function:: Involved in catalytic activity
Specific function:: Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP)
Gene Name:: ispD
Uniprot ID:: Q46893
Molecular weight:: 25737

Reactions

CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.

Protein Details

10. Protein gutQ

General function:: Involved in catalytic activity
Specific function:: Specific function unknown
Gene Name:: gutQ
Uniprot ID:: P17115
Molecular weight:: 34031

Reactions

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

Protein Details

11. Protein sgcE

General function:: Involved in catalytic activity
Specific function:: Probable pentose-5-phosphate 3-epimerase
Gene Name:: sgcE
Uniprot ID:: P39362
Molecular weight:: 23214

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D-Ribulose 5-phosphate (M2MDB000638)

Structure for #<Compound:0x987f8300>

Enzymes

Reactions

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