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Human Metabolome Database Version 2.5

 

Showing metabocard for Orotidylic acid (HMDB00218)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:57:46
Accession Number HMDB00218
Secondary Accession Numbers Not Available
Common Name Orotidylic acid
Description Orotidylic acid (OMP), is a pyrimidine nucleotide which is the last intermediate in the biosynthesis of uridine monophosphate. Decarboxylation by Orotidylate decarboxylase affords Uridine 5'-phosphate which is the route to Uridine and its derivatives de novo and consequently one of the most important processes in nucleic acid synthesis (Dictionary of Organic Compounds). In humans, the enzyme UMP synthase converts OMP into uridine 5'- monophosphate. If UMP synthase is defective, orotic aciduria can result. (Wikipedia)
Synonyms
  1. 5'-OMP
  2. OMP
  3. Ometoprim
  4. Orotidine 5'-monophosphate
  5. Orotidine 5'-phosphate
  6. Orotidine monophosphate
  7. Orotidylate
  8. Orotidylic acid
  9. 6-carboxy-5'-uridylic acid
  10. 6-carboxy-5'-uridylate
  11. 5-(Dihydrogen phosphate)orotidine
  12. 5'-(dihydrogen phosphate) Orotidine
  13. 5'-phosphate Orotidine
  14. orotidine-5'-phosphate
  15. 5'-(dihydrogen phosphate) 6-carboxy-uridine
  16. Omp (nucleotide)
  17. orotidine 5'-(dihydrogen phosphate)
  18. 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylic acid
  19. 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylic acid
  20. 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylate
  21. 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylate
  22. 2,6-dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  23. 2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
Chemical IUPAC Name 3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-dioxopyrimidine-4-carboxylic acid
Chemical Formula C10H13N2O11P
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Nucleosides and Nucleoside conjugates
Class
  • Nucleotides
Sub Class
  • Nucleotide monophosphates
Family
  • Mammalian Metabolite
Species
  • secondary alcohol
  • 1,2-diol
  • carboxylic acid
  • oxo(het)arene
  • phosphoric acid ester
  • aromatic compound
  • heterocyclic compound
Biofunction
  • Component of Pyrimidine metabolism
Application
—
Source
  • Endogenous
Average Molecular Weight 368.191
Monoisotopic Molecular Weight 368.025696
Isomeric SMILES O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)N1C(=O)NC(=O)C=C1C(O)=O
Canonical SMILES OC1C(O)C(OC1COP(O)(O)=O)N1C(=O)NC(=O)C=C1C(O)=O
KEGG Compound ID C01103 Link Image
BioCyc ID OROTIDINE-5-PHOSPHATE Link Image
BiGG ID 36813 Link Image
Wikipedia Link Orotidylic acid Link Image
NuGOwiki Link HMDB00218 Link Image
Metagene Link HMDB00218 Link Image
METLIN ID 5228 Link Image
PubChem Compound 160617 Link Image
PubChem Substance 824464 Link Image
ChEBI ID 15842 Link Image
CAS Registry Number 2149-82-8
InChI Identifier InChI=1/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1
Synthesis Reference Ueda, Tohru; Yamamoto, Miyako; Yamane, Akira; Imazawa, Masaoki; Inoue, Hideo. Nucleosides and nucleotides. XXIII. Conversion of uridine nucleotides to the 6-cyano derivatives: synthesis of orotidylic acid. Journal of Carbohydrates, Nucleosides, Nucleotides (1978), 5(3), 261-71.
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 8.61 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -3
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -4.1 [Predicted by PubChem via XLOGP]; -1.67 [Predicted by ALOGPS] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
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
Biofluid Location
  • Prostate Tissue
Tissue Location Not Available
Concentrations (Normal) Not Available
Concentrations (Abnormal)
Biofluid Prostate Tissue
Value 0.5 (0.0-1.0) umol/gr tissue
Age Adult:>18 yrs old
Sex Both
Condition Prostate cancer
Comments Estimated concentration
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. [PubMed Link Image]
Associated Disorders
Condition References
Prostate cancer
  • 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 Link Image]
OMIM ID
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 Link Image map00240 Link Image
General References
  1. Traut TW: Uridine-5'-phosphate synthase: evidence for substrate cycling involving this bifunctional protein. Arch Biochem Biophys. 1989 Jan;268(1):108-15. [PubMed Link Image]
  2. Wikipedia Link Image
Metabolic Enzymes
  1. Uridine monophosphate synthetase (Orotate phosphoribosyl transferase and orotidine-5'-decarboxylase), isoform CRA_b
Enzyme 1 [top]
Enzyme 1 ID 13096
Enzyme 1 Name Uridine monophosphate synthetase (Orotate phosphoribosyl transferase and orotidine-5'-decarboxylase), isoform CRA_b
Enzyme 1 Synonyms
  1. SubName: Uridine monophosphate synthetase isoform A
  2. SubName: cDNA FLJ75687, highly similar to Homo sapiens uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase) (UMPS), mRNA
Enzyme 1 Gene Name UMPS
Enzyme 1 Protein Sequence >Uridine monophosphate synthetase (Orotate phosphoribosyl transferase and orotidine-5'-decarboxylase), isoform CRA_b 
MAVARAALGPLVTGLYDVQAFKFGDFVLKSGLSSPIYIDLRGIVSRPRLLSQVADILFQT
AQNAGISFDTVCGVPYTALPLATVICSTNQIPMLIRRKETKDYGTKRLVEGTINPGETCL
IIEDVVTSGSSVLETVEVLQKEGLKVTDAIVLLDREQGGKDKLQAHGIRLHSVCTLSKML
EILEQQKKVDAETVGRVKRFIQENVFVAANHNGSPLSIKEAPKELSFGARAELPRIHPVA
SKLLRLMQKKETNLCLSADVSLARELLQLADALGPSICMLKTHVDILNDFTLDVMKELIT
LAKCHEFLIFEDRKFADIGNTVKKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLP
LHRGCLLIAEMSSTGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQ
LEAGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWEAYLSRLGV
Enzyme 1 Number of Residues 480
Enzyme 1 Molecular Weight 52221.1
Enzyme 1 Theoretical pI 7.26
Enzyme 1 GO Classification
Function
  • carbon-carbon lyase activity
  • carboxy-lyase activity
  • catalytic activity
  • lyase activity
  • orotate phosphoribosyltransferase activity
  • orotidine-5'-phosphate decarboxylase activity
  • transferase activity
  • transferase activity, transferring glycosyl groups
  • transferase activity, transferring pentosyl groups
Process
  • 'de novo' UMP biosynthetic process
  • 'de novo' pyrimidine base biosynthetic process
  • UMP biosynthetic process
  • cellular aromatic compound metabolic process
  • cellular metabolic process
  • cellular nitrogen compound metabolic process
  • metabolic process
  • nitrogen compound metabolic process
  • nucleobase metabolic process
  • nucleobase, nucleoside and nucleotide metabolic process
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
  • nucleoside metabolic process
  • nucleoside phosphate metabolic process
  • nucleotide metabolic process
  • pyrimidine base biosynthetic process
  • pyrimidine base metabolic process
  • pyrimidine nucleoside monophosphate biosynthetic process
  • pyrimidine nucleotide biosynthetic process
  • pyrimidine nucleotide metabolic process
  • pyrimidine ribonucleoside monophosphate biosynthetic process
Component
—
Enzyme 1 General Function Involved in catalytic activity
Enzyme 1 Specific Function Not Available
Enzyme 1 Pathways Not Available
Enzyme 1 Reactions Not Available
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 158256048 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID A8K5J1 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name A8K5J1_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1443 bp 
ATGGCGGTCGCTCGTGCAGCTTTGGGGCCATTGGTGACGGGTCTGTACGACGTGCAGGCT
TTCAAGTTTGGGGACTTCGTGCTGAAGAGCGGGCTTTCCTCCCCCATCTACATCGATCTG
CGGGGCATCGTGTCTCGACCGCGTCTTCTGAGTCAGGTTGCAGATATTTTATTCCAAACT
GCCCAAAATGCAGGCATCAGTTTTGACACCGTGTGTGGAGTGCCTTATACAGCTTTGCCA
TTGGCTACAGTTATCTGTTCAACCAATCAAATTCCAATGCTTATTAGAAGGAAAGAAACA
AAGGATTATGGAACTAAGCGTCTTGTAGAAGGAACTATTAATCCAGGAGAAACCTGTTTA
ATCATTGAAGATGTTGTCACCAGTGGATCTAGTGTTTTGGAAACTGTTGAGGTTCTTCAG
AAGGAGGGCTTGAAGGTCACTGATGCCATAGTGCTGTTGGACAGAGAGCAGGGAGGCAAG
GACAAGTTGCAGGCGCACGGGATCCGCCTCCACTCAGTGTGTACATTGTCCAAAATGCTG
GAGATTCTCGAGCAGCAGAAAAAAGTTGATGCTGAGACAGTTGGGAGAGTGAAGAGGTTT
ATTCAGGAGAATGTCTTTGTGGCAGCGAATCATAATGGTTCTCCCCTTTCTATAAAGGAA
GCACCCAAAGAACTCAGCTTCGGTGCACGTGCAGAGCTGCCCAGGATCCACCCAGTTGCA
TCGAAGCTTCTCAGGCTTATGCAAAAGAAGGAGACCAATCTGTGTCTATCTGCTGATGTT
TCACTGGCCAGAGAGCTGTTGCAGCTAGCAGATGCTTTAGGACCTAGTATCTGCATGCTG
AAGACTCATGTAGATATTTTGAATGATTTTACTCTGGATGTGATGAAGGAGTTGATAACT
CTGGCAAAATGCCATGAGTTCTTGATATTTGAAGACCGGAAGTTTGCAGATATAGGAAAC
ACAGTGAAAAAGCAGTATGAAGGAGGTATCTTTAAAATAGCTTCCTGGGCAGATCTAGTA
AATGCTCACGTGGTGCCAGGCTCAGGAGTTGTGAAAGGCCTGCAAGAAGTGGGCCTGCCT
TTGCATCGGGGGTGCCTCCTTATTGCGGAAATGAGCTCCACCGGCTCCCTGGCCACTGGG
GACTACACTAGAGCAGCGGTTAGAATGGCTGAGGAGCACTCTGAATTTGTTGTTGGTTTT
ATTTCTGGCTCCCGAGTAAGCATGAAACCAGAATTTCTTCACTTGACTCCAGGAGTTCAG
TTGGAAGCAGGAGGAGATAATCTTGGCCAACAGTACAATAGCCCACAAGAAGTTATTGGC
AAACGAGGTTCCGATATCATCATTGTAGGTCGTGGCATAATCTCAGCAGCTGATCGTCTG
GAAGCAGCAGAGATGTACAGAAAAGCTGCTTGGGAAGCGTATTTGAGTAGACTTGGTGTT
TGA
Enzyme 1 GenBank Gene ID AK291306 Link Image
Enzyme 1 GeneCard ID UMPS Link Image
Enzyme 1 GenAtlas ID UMPS Link Image
Enzyme 1 HGNC ID HGNC:12563 Link Image
Enzyme 1 Chromosome Location 3
Enzyme 1 Locus 3q13
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X: The sequence of the human genome. Science. 2001 Feb 16;291(5507):1304-51. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available