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Human Metabolome Database Version 2.5

 

Showing metabocard for dUDP (HMDB01000)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:58:25
Accession Number HMDB01000
Secondary Accession Numbers Not Available
Common Name dUDP
Description dUDP is a derivative of nucleic acid UTP, in which the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose has been removed (hence the deoxy- part of the name). Additionally, the diphosphate of the name indicates that one of the phosphoryl groups of UTP has been removed, most likely by hydrolysis (Wikipedia).
Synonyms
  1. 2'-deoxyuridine-5'-diphosphate
  2. dUDP
  3. deoxyuridine-diphosphate
Chemical IUPAC Name [[5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxyphosphonic acid
Chemical Formula C9H14N2O11P2
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Nucleosides and Nucleoside conjugates
Class
  • Nucleotides
Sub Class
  • Nucleotide diphosphates
Family
  • Mammalian Metabolite
Species
  • secondary alcohol
  • oxo(het)arene
  • phosphoric acid ester
  • aromatic compound
  • heterocyclic compound
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 388.162
Monoisotopic Molecular Weight 388.007294
Isomeric SMILES O[C@H]1C[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
Canonical SMILES OC1CC(OC1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
KEGG Compound ID Not Available
BioCyc ID DUDP Link Image
BiGG ID 37403 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB01000 Link Image
Metagene Link HMDB01000 Link Image
METLIN ID 5931 Link Image
PubChem Compound 687 Link Image
PubChem Substance 6822189 Link Image
ChEBI ID Not Available
CAS Registry Number 4208-67-7
InChI Identifier InChI=1/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Synthesis Reference Not Available
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 8.03 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -3
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -0.99 [Predicted by ALOGPS]; -4.4 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show
SDF File Show
PDB File Show
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
  • mitochondria
  • nucleus
Biofluid Location
  • Blood
Tissue Location Not Available
Concentrations (Normal)
Biofluid Blood
Value 0.5 +/- 0.1 uM
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Traut TW: Physiological concentrations of purines and pyrimidines. Mol Cell Biochem. 1994 Nov 9;140(1):1-22. [PubMed Link Image]
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 Link Image map00240 Link Image
General References
  1. Diaz C, Valverde L, Brenes O, Rucavado A, Gutierrez JM: Characterization of events associated with apoptosis/anoikis induced by snake venom metalloproteinase BaP1 on human endothelial cells. J Cell Biochem. 2005 Feb 15;94(3):520-8. [PubMed Link Image]
  2. Lambard S, Galeraud-Denis I, Martin G, Levy R, Chocat A, Carreau S: Analysis and significance of mRNA in human ejaculated sperm from normozoospermic donors: relationship to sperm motility and capacitation. Mol Hum Reprod. 2004 Jul;10(7):535-41. Epub 2004 Apr 20. [PubMed Link Image]
  3. Wang J, Ohara N, Takekida S, Xu Q, Maruo T: Comparative effects of heparin-binding epidermal growth factor-like growth factor on the growth of cultured human uterine leiomyoma cells and myometrial cells. Hum Reprod. 2005 Jun;20(6):1456-65. Epub 2005 Mar 10. [PubMed Link Image]
  4. Di Simone N, Riccardi P, Maggiano N, Piacentani A, D'Asta M, Capelli A, Caruso A: Effect of folic acid on homocysteine-induced trophoblast apoptosis. Mol Hum Reprod. 2004 Sep;10(9):665-9. Epub 2004 Jul 30. [PubMed Link Image]
  5. Duran EH, Morshedi M, Taylor S, Oehninger S: Sperm DNA quality predicts intrauterine insemination outcome: a prospective cohort study. Hum Reprod. 2002 Dec;17(12):3122-8. [PubMed Link Image]
  6. Henkel R, Hajimohammad M, Stalf T, Hoogendijk C, Mehnert C, Menkveld R, Gips H, Schill WB, Kruger TF: Influence of deoxyribonucleic acid damage on fertilization and pregnancy. Fertil Steril. 2004 Apr;81(4):965-72. [PubMed Link Image]
Metabolic Enzymes
  1. Thymidylate kinase
  2. Nucleoside diphosphate kinase 6
  3. Ribonucleoside-diphosphate reductase subunit M2 B
Enzyme 1 [top]
Enzyme 1 ID 5312
Enzyme 1 Name Thymidylate kinase
Enzyme 1 Synonyms
  1. dTMP kinase
Enzyme 1 Gene Name DTYMK
Enzyme 1 Protein Sequence >Thymidylate kinase 
MAARRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKK
SDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQP
DVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQERALRCFHQLMKDTTLNWKMVDA
SKSIEAVHEDIRVLSEDAIRTATEKPLGELWK
Enzyme 1 Number of Residues 212
Enzyme 1 Molecular Weight 23820
Enzyme 1 Theoretical pI 8.49
Enzyme 1 GO Classification
Function
  • ATP binding
  • adenyl nucleotide binding
  • binding
  • catalytic activity
  • nucleotide binding
  • phosphotransferase activity, phosphate group as acceptor
  • purine nucleotide binding
  • thymidylate kinase activity
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
  • cellular metabolism
  • dTDP biosynthesis
  • dTTP biosynthesis
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • nucleotide metabolism
  • physiological process
  • pyrimidine deoxyribonucleoside diphosphate biosynthesis
  • pyrimidine deoxyribonucleoside triphosphate biosynthesis
  • pyrimidine nucleoside diphosphate biosynthesis
  • pyrimidine nucleoside triphosphate biosynthesis
  • pyrimidine nucleotide biosynthesis
  • pyrimidine nucleotide metabolism
Component
—
Enzyme 1 General Function Nucleotide transport and metabolism
Enzyme 1 Specific Function Catalyzes the conversion of dTMP to dTDP
Enzyme 1 Pathways
Enzyme 1 Reactions
  • ATP + dTMP = ADP + dTDP
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 37206 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P23919 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name DTYMK_HUMAN Link Image
Enzyme 1 PDB ID 1E9A Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >636 bp 
ATGGCGGCCCGGCGCGGGGCTCTCATAGTGCTGGAGGGCGTGGACCGCGCCGGGAAGAGC
ACGCAGAGCCGCAAGCTGGTGGAAGCGCTGTCGCGCGGGCCACCGCCCGAACTGCTCCGG
TTCCCGGAAAGATCAACTGAAATCGGCAAACTTCTGAGTTCCTACTTGCAAAAGAAAAGT
GACGTGGAGGATCACTCGGTGCACCTGCTTTTTTCTGCAAATCGCTGGGAACAAGTGCCG
TTAATTAAGGAAAAGTTGAGCCAGGGCGTGACCCTCGTCGTGGACAGATACGCATTTTCT
GGTGTGGCCTTCACCGGTGCCAAGGAGAATTTTTCCCTAGACTGGTGTAAACAGCCAGAC
GTGGGCCTTCCCAAACCCGACCTGGTCCTGTTCCTCCAGTTACAGCTGGCGGATGCTGCC
AAGCGGGGAGCGTTTGGCCATGAGCGCTATGAGAACGGGGCTTTCCAGGAGCGGGCGCTC
CGGTGTTTCCACCAGCTCATGAAAGACACGACTTTGAACTGGAAGATGGTGGATGCTTCC
AAAAGACTCGAAGCTGTCCATGAGGAACTCCGCGTGCTCTCTGAGGACGCCATCCGCACT
GCCACAGAGAAGCCGCTGGGGGAGCTATGGAAGTGA
Enzyme 1 GenBank Gene ID X54729 Link Image
Enzyme 1 GeneCard ID DTYMK Link Image
Enzyme 1 GenAtlas ID DTYMK Link Image
Enzyme 1 HGNC ID HGNC:3061 Link Image
Enzyme 1 Chromosome Location 2
Enzyme 1 Locus 2q37.3
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Su JY, Sclafani RA: Molecular cloning and expression of the human deoxythymidylate kinase gene in yeast. Nucleic Acids Res. 1991 Feb 25;19(4):823-7. [PubMed Link Image]
  2. Huang SH, Tang A, Drisco B, Zhang SQ, Seeger R, Li C, Jong A: Human dTMP kinase: gene expression and enzymatic activity coinciding with cell cycle progression and cell growth. DNA Cell Biol. 1994 May;13(5):461-71. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 5346
Enzyme 2 Name Nucleoside diphosphate kinase 6
Enzyme 2 Synonyms
  1. NDK 6
  2. NDP kinase 6
  3. nm23-H6
  4. Inhibitor of p53-induced apoptosis-alpha
  5. IPIA-alpha
Enzyme 2 Gene Name NME6
Enzyme 2 Protein Sequence >Nucleoside diphosphate kinase 6 
MASILRSPQALQLTLALIKPDAVAHPLILEAVHQQILSNKFLIVRMRELLWRKEDCQRFY
REHEGRFFYQRLVEFMASGPIRAYILAHKDAIQLWRTLMGPTRVFRARHVAPDSIRGSFG
LTDTRNTTHGSDSVVSASREIAAFFPDFSEQRWYEEEEPQLRCGPVCYSPEGGVHYVAGT
GGLGPA
Enzyme 2 Number of Residues 186
Enzyme 2 Molecular Weight 21142
Enzyme 2 Theoretical pI 8.49
Enzyme 2 GO Classification
Function
  • ATP binding
  • adenyl nucleotide binding
  • binding
  • catalytic activity
  • ion binding
  • magnesium ion binding
  • metal ion binding
  • nucleoside diphosphate kinase activity
  • nucleotide binding
  • phosphotransferase activity, phosphate group as acceptor
  • purine nucleotide binding
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
  • CTP biosynthesis
  • GTP biosynthesis
  • UTP biosynthesis
  • cellular metabolism
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • nucleoside triphosphate biosynthesis
  • nucleoside triphosphate metabolism
  • nucleotide metabolism
  • physiological process
  • purine nucleoside triphosphate biosynthesis
  • purine nucleotide biosynthesis
  • purine nucleotide metabolism
  • purine ribonucleoside triphosphate biosynthesis
  • pyrimidine ribonucleoside triphosphate biosynthesis
  • ribonucleoside triphosphate biosynthesis
Component
—
Enzyme 2 General Function Nucleotide transport and metabolism
Enzyme 2 Specific Function Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Inhibitor of p53-induced apoptosis
Enzyme 2 Pathways
Enzyme 2 Reactions
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • 1-24
Enzyme 2 Transmembrane Regions Not Available
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 3228530 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID O75414 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name NDK6_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >561 bp 
ATGGCCTCAATCTTGCGAAGCCCTCAGGCTCTCCAGCTCACTCTAGCCCTGATCAAGCCT
GACGCAGTCGCCCATCCACTGATTCTGGAGGCTGTTCATCAGCAGATTCTAAGCAACAAG
TTCCTGATTGTACGAATGAGAGAACTACTGTGGAGAAAGGAAGATTGCCAGAGGTTTTAC
CGAGAGCATGAAGGGCGTTTTTTCTATCAGAGGCTGGTGGAGTTCATGGCCAGCGGGCCA
ATCCGAGCCTACATCCTTGCCCACAAGGATGCCATCCAGCTCTGGAGGACGCTCATGGGA
CCCACCAGAGTGTTCCGAGCACGCCATGTGGCCCCAGATTCTATCCGTGGGAGTTTCGGC
CTCACTGACACCCGCAACACCACCCATGGTTCGGACTCTGTGGTTTCAGCCAGCAGAGAG
ATTGCAGCCTTCTTCCCTGACTTCAGTGAACAGCGCTGGTATGAGGAGGAAGAGCCCCAG
TTGCGCTGTGGCCCTGTGTGCTATAGCCCAGAGGGAGGTGTCCACTATGTAGCTGGAACA
GGAGGCCTAGGACCAGCCTGA
Enzyme 2 GenBank Gene ID AF051941 Link Image
Enzyme 2 GeneCard ID NME6 Link Image
Enzyme 2 GenAtlas ID NME6 Link Image
Enzyme 2 HGNC ID HGNC:20567 Link Image
Enzyme 2 Chromosome Location 3
Enzyme 2 Locus 3p21
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Mehus JG, Deloukas P, Lambeth DO: NME6: a new member of the nm23/nucleoside diphosphate kinase gene family located on human chromosome 3p21.3. Hum Genet. 1999 Jun;104(6):454-9. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 13094
Enzyme 3 Name Ribonucleoside-diphosphate reductase subunit M2 B
Enzyme 3 Synonyms
  1. TP53- inducible ribonucleotide reductase M2 B
  2. p53-inducible ribonucleotide reductase small subunit 2-like protein
  3. p53R2
Enzyme 3 Gene Name RRM2B
Enzyme 3 Protein Sequence >Ribonucleoside-diphosphate reductase subunit M2 B 
MGDPERPEAAGLDQDERSSSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQ
ASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEA
RCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRK
STFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQ
YLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFS
KVFQAENPFDFMENISLEGKTNFFEKRVSEYQRFAVMAETTDNVFTLDADF
Enzyme 3 Number of Residues 351
Enzyme 3 Molecular Weight 40737
Enzyme 3 Theoretical pI 4.61
Enzyme 3 GO Classification
Function
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on CH2 groups
  • oxidoreductase activity, acting on CH2 groups, disulfide as acceptor
  • ribonucleoside-diphosphate reductase activity
Process
  • cellular metabolism
  • deoxyribonucleoside diphosphate metabolism
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • nucleoside diphosphate metabolism
  • nucleotide metabolism
  • physiological process
Component
—
Enzyme 3 General Function Nucleotide transport and metabolism
Enzyme 3 Specific Function Plays a pivotal role in cell survival by repairing damaged DNA in a p53/TP53-dependent manner. Supplies deoxyribonucleotides for DNA repair in cells arrested at G1 or G2. Contains an iron-tyrosyl free radical center required for catalysis. Forms an active ribonucleotide reductase (RNR) complex with RRM1 which is expressed both in resting and proliferating cells in response to DNA damage
Enzyme 3 Pathways
Enzyme 3 Reactions
  • 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin [RN:R04294] ALL_REAC R04294 > R02017 R02018 R02019 R02024
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein 7229086 Link Image
Enzyme 3 UniProtKB/Swiss-Prot ID Q7LG56 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name RIR2B_HUMAN Link Image
Enzyme 3 PDB ID Not Available
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID AB036063 Link Image
Enzyme 3 GeneCard ID Q7LG56 Link Image
Enzyme 3 GenAtlas ID RRM2B Link Image
Enzyme 3 HGNC ID HGNC:17296 Link Image
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References
  1. Tanaka H, Arakawa H, Yamaguchi T, Shiraishi K, Fukuda S, Matsui K, Takei Y, Nakamura Y: A ribonucleotide reductase gene involved in a p53-dependent cell-cycle checkpoint for DNA damage. Nature. 2000 Mar 2;404(6773):42-9. [PubMed Link Image]
Enzyme 3 Metabolite References Not Available