ECMDB: D-Arabinose 5-phosphate (ECMDB11734) (M2MDB000821)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (3)XML

Proteins (228)

Record Information

Version

2.0

Creation Date

2012-05-31 14:20:39 -0600

Update Date

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

Secondary Accession Numbers

ECMDB11734

Identification

Name:

D-Arabinose 5-phosphate

Description

D-Arabinose 5-phosphate is an intermediate in biosynthesis of lipopolysaccharide.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

Ara5P
Arabinose 5-phosphate
Arabinose 5-phosphoric acid
Arabinose-5-P
Arabinose-5P
D-A-5-P
D-Arabinose 5-phosphate
D-Arabinose 5-phosphoric acid
D-Arabinose-5-P

Chemical Formula:

C₅H₁₁O₈P

Weight:

Average: 230.1098
Monoisotopic: 230.01915384

InChI Key:

PPQRONHOSHZGFQ-WDCZJNDASA-N

InChI:

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1

CAS number:

13137-52-5

IUPAC Name:

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

Traditional IUPAC Name:

arabinose 5-phosphate

SMILES:

O[C@H](COP(O)(O)=O)[C@@H](O)[C@H](O)C=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
Monosaccharide phosphate
Monoalkyl phosphate
Beta-hydroxy aldehyde
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Hydrocarbon derivative
Aldehyde
Organic oxide
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

D-arabinose 5-phosphate (CHEBI:16241 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	19.3 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-3.1	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-3.5	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	42.26 m³·mol⁻¹	ChemAxon
Polarizability	18 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:

SMPDB Pathways:

Lipopolysaccharide biosynthesis	PW000831
lipopolysaccharide biosynthesis II	PW001905
lipopolysaccharide biosynthesis III	PW002059

KEGG Pathways:

Lipopolysaccharide biosynthesis ec00540
Metabolic pathways eco01100

EcoCyc Pathways:

CMP-KDO biosynthesis I PWY-1269

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
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-EI-TOF (Non-derivatized)	splash10-014j-0954000000-13c360ef6d50c290ff75	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1954000000-66deca60c06849233c1e	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-0954000000-13c360ef6d50c290ff75	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1954000000-66deca60c06849233c1e	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9100000000-b771da2f9bcb85359615	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-01c0-2934100000-c0832bdf2f33a1c2e0ae	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 (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-1090000000-31e1af2994eda21a1bc4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9100000000-2045507193c154fa6155	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-002b-9000000000-ea919a44fa730a6b30ac	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-585f803ae9cdd8a87b5b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-39ddb0bbc9b7b081c7fd	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-002b-9000000000-f3fe9e7cc40f16c3578e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-e3a1ec95af6dcad460c7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-82ac7295f5c79a94ec38	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-352da97e65dd9cc16df9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004j-9040000000-0b86189542286f55e20f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9000000000-98c2dab693f3635a82c4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3690000000-06b766b00394897d8276	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-6f93a4202efb7ba3d3fd	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-a324e9f10ad080e0ea34	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001j-9540000000-adbdd8414bace2c44f56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9200000000-b929bd8d4139b2fa147a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9000000000-cbffc4c85bf45fc4aeef	View in MoNA
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
1D NMR	1H 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
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
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. Pubmed: 19212411
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	16241
HMDB ID	HMDB11734
Pubchem Compound ID	230
Kegg ID	C01112
ChemSpider ID	163687
Wikipedia ID	Not Available
BioCyc ID	ARABINOSE-5P
EcoCyc ID	ARABINOSE-5P

Enzymes

Protein Details

1. 2-dehydro-3-deoxyphosphooctonate aldolase

General function:: Involved in catalytic activity
Specific function:: Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth
Gene Name:: kdsA
Uniprot ID:: P0A715
Molecular weight:: 30833

Reactions

Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate.

Protein Details

2. 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

3. 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.

D-Arabinose 5-phosphate (ECMDB11734) (M2MDB000821)

Structure for #<Compound:0xa2fc090c>

Enzymes

Reactions

Reactions

Reactions