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Human Metabolome Database Version 2.5

 

Showing metabocard for Deoxyribose 5-phosphate (HMDB01031)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:58:27
Accession Number HMDB01031
Secondary Accession Numbers Not Available
Common Name Deoxyribose 5-phosphate
Description Deoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source.
Synonyms
  1. 2-deoxy-alpha-D-ribose 5-phosphate
  2. 2-deoxy-d-ribose-5-phosphate
  3. 2-deoxyribose-5-p
  4. 2-deoxyribose-5-phosphate
  5. Deoxyribose 5-phosphate
  6. Deoxyribose 5-phosphic acid
  7. deoxy-ribose-5p
  8. deoxyribose-5-p
  9. deoxyribose-5-phosphate
  10. 2-deoxy-alpha-delta-ribose 5-phosphate
  11. 2-Deoxy-D-ribose 5-phosphate
  12. 2-deoxyribose 5-phosphate
Chemical IUPAC Name (3,5-dihydroxyoxolan-2-yl)methoxyphosphonic acid
Chemical Formula C5H11O7P
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Carbohydrates and Carbohydrate conjugates
Class
  • Sugar Phosphates
Sub Class
  • Monosaccharide phosphates
Family
  • Mammalian Metabolite
Species
  • hemiacetal
  • secondary alcohol
  • phosphoric acid ester
  • heterocyclic compound
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 214.110
Monoisotopic Molecular Weight 214.024246
Isomeric SMILES O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
Canonical SMILES OC1CC(O)C(COP(O)(O)=O)O1
KEGG Compound ID C00673 Link Image
BioCyc ID DEOXY-RIBOSE-5P Link Image
BiGG ID 35666 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB01031 Link Image
Metagene Link HMDB01031 Link Image
METLIN ID 5956 Link Image
PubChem Compound 635 Link Image
PubChem Substance 2616 Link Image
ChEBI ID 16132 Link Image
CAS Registry Number 102916-66-5
InChI Identifier InChI=1/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1
Synthesis Reference Method of preparing 2-deoxyribose 5-phosphate US Patent #7270992
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 37.5 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -2
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -2.14 [Predicted by ALOGPS]; -2.9 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show Link Image
SDF File Show Link Image
PDB File Show Link Image
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
Biofluid Location Not Available
Tissue Location Not Available
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
Pentose Phosphate Pathway SMP00031 Link Image map00030 Link Image
General References Not Available
Metabolic Enzymes
  1. Putative deoxyribose-phosphate aldolase
  2. Ribokinase
Enzyme 1 [top]
Enzyme 1 ID 6233
Enzyme 1 Name Putative deoxyribose-phosphate aldolase
Enzyme 1 Synonyms
  1. Phosphodeoxyriboaldolase
  2. DERA
  3. Deoxyriboaldolase
Enzyme 1 Gene Name DERA
Enzyme 1 Protein Sequence >Putative deoxyribose-phosphate aldolase 
MSAHNRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLS
GDDTSSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNI
PVASVAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRK
ACGEAHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAI
RDFFWKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQ
IYHHVTGRYAAYHDLPMS
Enzyme 1 Number of Residues 318
Enzyme 1 Molecular Weight 35230.4
Enzyme 1 Theoretical pI 9.31
Enzyme 1 GO Classification
Function
  • aldehyde-lyase activity
  • carbon-carbon lyase activity
  • catalytic activity
  • deoxyribose-phosphate aldolase activity
  • lyase activity
Process
  • cellular nitrogen compound metabolic process
  • deoxyribonucleotide catabolic process
  • metabolic process
  • nitrogen compound metabolic process
  • nucleobase, nucleoside and nucleotide metabolic process
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
  • nucleoside phosphate metabolic process
  • nucleotide catabolic process
  • nucleotide metabolic process
Component
  • cell part
  • cytoplasm
  • intracellular part
Enzyme 1 General Function Involved in catalytic activity
Enzyme 1 Specific Function 2-deoxy-D-ribose 5-phosphate = D- glyceraldehyde 3-phosphate + acetaldehyde
Enzyme 1 Pathways
Enzyme 1 Reactions
  • 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde [RN:R01066]
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 116063554 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q9Y315 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name DEOC_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >957 bp 
ATGTCCGCGCACAATCGGGGCACCGAGCTCGACCTTAGCTGGATCTCCAAAATACAAGTG
AATCACCCGGCAGTTCTGAGGCGTGCGGAACAAATCCAGGCTCGCAGAACCGTGAAAAAG
GAGTGGCAGGCTGCTTGGCTCCTGAAAGCTGTTACCTTTATAGATCTTACTACACTTTCA
GGTGATGATACATCTTCCAACATTCAAAGGCTCTGTTATAAAGCCAAATACCCAATCCGG
GAAGATCTCTTAAAAGCTTTAAATATGCATGATAAAGGCATTACTACAGCCGCCGTTTGT
GTTTATCCCGCCCGGGTGTGTGATGCTGTAAAAGCACTCAAGGCTGCAGGCTGTAATATC
CCTGTGGCATCAGTGGCCGCTGGATTTCCAGCTGGACAGACTCATTTGAAGACACGATTA
GAAGAGATCAGATTGGCTGTGGAAGATGGAGCTACAGAAATCGACGTGGTAATTAACAGA
AGCTTGGTGCTGACAGGCCAGTGGGAAGCCCTGTATGATGAGATTCGTCAGTTTCGCAAG
GCCTGTGGGGAGGCTCATCTTAAAACTATATTAGCGACAGGAGAACTTGGAACTCTTACT
AATGTCTATAAAGCCAGTATGATAGCAATGATGGCAGGATCAGATTTTATTAAGACCTCT
ACTGGAAAAGAAACAGTAAATGCCACCTTCCCGGTAGCTATAGTAATGCTGCGGGCCATT
AGAGATTTCTTCTGGAAAACTGGAAACAAGATAGGGTTTAAACCAGCAGGAGGCATCCGC
AGTGCAAAGGATTCCCTTGCTTGGCTCTCTCTTGTAAAGGAGGAGCTTGGAGATGAGTGG
CTGAAGCCAGAACTCTTTCGAATAGGTGCCAGTACTCTGCTCTCGGACATTGAGAGGCAG
ATTTACCATCATGTGACTGGAAGATATGCAGCTTATCATGATCTTCCAATGTCTTAA
Enzyme 1 GenBank Gene ID NM_015954.2 Link Image
Enzyme 1 GeneCard ID DERA Link Image
Enzyme 1 GenAtlas ID DERA Link Image
Enzyme 1 HGNC ID HGNC:24269 Link Image
Enzyme 1 Chromosome Location 1
Enzyme 1 Locus 12p12.3
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Lai CH, Chou CY, Ch'ang LY, Liu CS, Lin W: Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Genome Res. 2000 May;10(5):703-13. [PubMed Link Image]
  2. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed Link Image]
  3. Imami K, Sugiyama N, Kyono Y, Tomita M, Ishihama Y: Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. Anal Sci. 2008 Jan;24(1):161-6. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 6377
Enzyme 2 Name Ribokinase
Enzyme 2 Synonyms Not Available
Enzyme 2 Gene Name RBKS
Enzyme 2 Protein Sequence >Ribokinase 
MAASGEPQRQWQEEVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCV
QAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNI
IVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAP
AIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEG
CVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAV
SVQAAGTQSSYPYKKDLPLTLF
Enzyme 2 Number of Residues 322
Enzyme 2 Molecular Weight 34142.7
Enzyme 2 Theoretical pI 4.68
Enzyme 2 GO Classification
Function
  • catalytic activity
  • phosphotransferase activity, alcohol group as acceptor
  • ribokinase activity
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
  • D-ribose metabolic process
  • alcohol metabolic process
  • metabolic process
  • monosaccharide metabolic process
  • pentose metabolic process
  • small molecule metabolic process
Component
—
Enzyme 2 General Function Involved in ribokinase activity
Enzyme 2 Specific Function ATP + D-ribose = ADP + D-ribose 5-phosphate
Enzyme 2 Pathways
Enzyme 2 Reactions
  • ATP + D-ribose = ADP + D-ribose 5-phosphate [RN:R01051]
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 10799803 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q9H477 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name RBSK_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >969 bp 
ATGGCGGCGTCTGGGGAACCCCAGAGGCAGTGGCAAGAGGAGGTGGCGGCGGTGGTAGTG
GTGGGCTCCTGCATGACCGACCTGGTCAGTCTTACTTCTCGTTTGCCAAAAACTGGAGAA
ACCATCCATGGACATAAGTTTTTTATTGGCTTTGGAGGGAAAGGTGCCAACCAGTGTGTC
CAAGCTGCTCGGCTTGGAGCAATGACGTCCATGGTGTGTAAGGTTGGCAAAGATTCTTTT
GGCAATGATTATATAGAAAACTTAAAACAGAATGATATTTCTACAGAATTTACATATCAG
ACTAAAGATGCTGCTACAGGAACTGCTTCTATAATTGTCAATAATGAAGGCCAGAATATC
ATTGTCATAGTGGCTGGAGCAAATTTACTTTTGAATACGGAGGATCTGAGGGCAGCAGCC
AATGTCATTAGCAGAGCCAAAGTCATGGTCTGCCAGCTCGAAATAACTCCAGCAACTTCT
TTGGAAGCCCTAACAATGGCCCGCAGGAGTGGAGTGAAAACCTTGTTCAATCCAGCCCCT
GCCATTGCTGACCTGGATCCCCAGTTCTACACCCTCTCAGATGTGTTCTGCTGCAATGAA
AGTGAGGCTGAGATTTTAACTGGCCTCACGGTGGGCAGCGCTGCAGATGCTGGGGAGGCT
GCATTAGTGCTCTTGAAAAGGGGCTGCCAGGTGGTAATCATTACCTTAGGGGCTGAAGGA
TGTGTGGTGCTGTCACAGACAGAACCTGAGCCAAAGCACATTCCCACAGAGAAAGTCAAG
GCTGTGGATACCACGGGTGCTGGTGACAGCTTTGTGGGAGCTCTGGCCTTCTACCTGGCT
TACTATCCAAATCTGTCCTTGGAAGACATGCTCAACAGATCCAATTTCATTGCAGCAGTC
AGTGTCCAGGCTGCAGGAACACAGTCATCTTACCCTTACAAAAAAGACCTTCCGCTTACT
CTGTTTTGA
Enzyme 2 GenBank Gene ID AJ404857 Link Image
Enzyme 2 GeneCard ID RBKS Link Image
Enzyme 2 GenAtlas ID RBKS Link Image
Enzyme 2 HGNC ID HGNC:30325 Link Image
Enzyme 2 Chromosome Location 2
Enzyme 2 Locus 2p23.3
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed Link Image]
  2. Park J, van Koeverden P, Singh B, Gupta RS: Identification and characterization of human ribokinase and comparison of its properties with E. coli ribokinase and human adenosine kinase. FEBS Lett. 2007 Jul 10;581(17):3211-6. Epub 2007 Jun 15. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available