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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:40:09 UTC
HMDB IDHMDB0001000
Secondary Accession Numbers
  • HMDB01000
Metabolite Identification
Common NamedUDP
DescriptiondUDP belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dUDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dUDP exists in all eukaryotes, ranging from yeast to humans. Within humans, dUDP participates in a number of enzymatic reactions. In particular, dUDP can be biosynthesized from deoxyuridine triphosphate through its interaction with the enzyme nucleoside diphosphate kinase 6. In addition, dUDP can be biosynthesized from dUMP; which is mediated by the enzyme thymidylate synthase. In humans, dUDP is involved in the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, dUDP has been detected, but not quantified in, several different foods, such as sour cherries, strawberries, cassava, pomes, and alpine sweetvetchs. This could make dUDP a potential biomarker for the consumption of these foods.
Structure
Data?1595280226
Synonyms
ValueSource
2'-Deoxyuridine 5'-diphosphateChEBI
2'-Deoxyuridine 5'-diphosphoric acidGenerator
2'-Deoxyuridine-5'-diphosphateHMDB
Deoxyuridine-diphosphateHMDB
2'-Deoxyuridine 5'-(trihydrogen diphosphate)HMDB
2’-Deoxyuridine 5’-(trihydrogen diphosphate)HMDB
2’-Deoxyuridine 5’-diphosphateHMDB
Deoxyuridine 5'-diphosphateHMDB
Deoxyuridine 5’-diphosphateHMDB
Deoxyuridine diphosphateHMDB
dUDPHMDB
Chemical FormulaC9H14N2O11P2
Average Molecular Weight388.1618
Monoisotopic Molecular Weight388.007282324
IUPAC Name[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional NamedUDP
CAS Registry Number4208-67-7
SMILES
O[C@H]1C[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/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
InChI KeyQHWZTVCCBMIIKE-SHYZEUOFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Lactam
  • Urea
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility8.03 g/LALOGPS
logP10(-0.99) g/LALOGPS
logP10(-2.1) g/LChemAxon
logS10(-1.7) g/LALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area192.16 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity72.8 m³·mol⁻¹ChemAxon
Polarizability29.83 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+183.5531661259
DarkChem[M-H]-176.69331661259
AllCCS[M+H]+179.06732859911
AllCCS[M-H]-172.52332859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
dUDP,1TMS,#1C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)OP(=O)(O)O3104.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TMS,#2C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)OP(=O)(O)O3181.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TMS,#3C[Si](C)(C)OP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O3164.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TMS,#4C[Si](C)(C)N1C(=O)C=CN([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)O)O2)C1=O3174.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TBDMS,#1CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1COP(=O)(O)OP(=O)(O)O3342.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TBDMS,#2CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O)OP(=O)(O)O3407.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TBDMS,#3CC(C)(C)[Si](C)(C)OP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O3401.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
dUDP,1TBDMS,#4CC(C)(C)[Si](C)(C)N1C(=O)C=CN([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(O)O)O2)C1=O3396.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - dUDP GC-MS (Non-derivatized) - 70eV, Positivesplash10-004m-6911000000-1f7795debc1eaf0802e62017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - dUDP GC-MS (1 TMS) - 70eV, Positivesplash10-002g-9741200000-2a5ff084260317ace5412017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - dUDP GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - dUDP GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 10V, Positive-QTOFsplash10-03di-1900000000-3d46a12380fc537ed4822016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 20V, Positive-QTOFsplash10-03di-4910000000-e4d9c69da2a4f1af3f7d2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 40V, Positive-QTOFsplash10-03di-6900000000-38fc58820b65e6b774812016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 10V, Negative-QTOFsplash10-0006-6309000000-e32a735e5de73376968b2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 20V, Negative-QTOFsplash10-056u-9801000000-189cbc835aaa1c3340b12016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 40V, Negative-QTOFsplash10-004i-9100000000-07b08a59c26df7bb2d1e2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 10V, Negative-QTOFsplash10-000i-0009000000-aa2d362ee8b723b7d4882021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 20V, Negative-QTOFsplash10-004i-9111000000-b30fec320d4d01519c032021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 40V, Negative-QTOFsplash10-004i-9000000000-5632c2fa3d2d7c954d902021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 10V, Positive-QTOFsplash10-03di-3913000000-cbd6b90181ad2dcbef102021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 20V, Positive-QTOFsplash10-03di-6910000000-514b52784d71478993f82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - dUDP 40V, Positive-QTOFsplash10-03di-4900000000-32241af48bd1f1fd6e372021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.5 +/- 0.1 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03413
Phenol Explorer Compound IDNot Available
FooDB IDFDB022361
KNApSAcK IDNot Available
Chemspider ID128553
KEGG Compound IDC01346
BioCyc IDDUDP
BiGG ID37403
Wikipedia LinkNot Available
METLIN ID5931
PubChem Compound145729
PDB IDNot Available
ChEBI ID28850
Food Biomarker OntologyNot Available
VMH IDDUDP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
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:15543558 ]
  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:15100385 ]
  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:15760954 ]
  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:15286211 ]
  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:12456611 ]
  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:15066449 ]
  7. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Only showing the first 10 proteins. There are 12 proteins in total.

Enzymes

General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the conversion of dTMP to dTDP.
Gene Name:
DTYMK
Uniprot ID:
P23919
Molecular weight:
23819.105
Reactions
Adenosine triphosphate + dUMP → ADP + dUDPdetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Molecular weight:
22760.43
Reactions
Deoxyuridine triphosphate + Uridine → dUDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Cytidine → dUDP + Cytidine monophosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:
NME4
Uniprot ID:
O00746
Molecular weight:
20658.45
Reactions
Adenosine triphosphate + dUDP → ADP + Deoxyuridine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
Reactions
Adenosine triphosphate + dUDP → ADP + Deoxyuridine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
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.
Gene Name:
NME7
Uniprot ID:
Q9Y5B8
Molecular weight:
42491.365
Reactions
Adenosine triphosphate + dUDP → ADP + Deoxyuridine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.
Gene Name:
NME2
Uniprot ID:
P22392
Molecular weight:
30136.92
Reactions
Adenosine triphosphate + dUDP → ADP + Deoxyuridine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
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. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.
Gene Name:
NME3
Uniprot ID:
Q13232
Molecular weight:
19014.85
Reactions
Adenosine triphosphate + dUDP → ADP + Deoxyuridine triphosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
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.
Gene Name:
NME6
Uniprot ID:
O75414
Molecular weight:
22002.965
Reactions
Adenosine triphosphate + dUDP → ADP + Deoxyuridine triphosphatedetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK2
Uniprot ID:
Q9BZX2
Molecular weight:
29298.92
Reactions
Deoxyuridine triphosphate + Uridine → dUDP + Uridine 5'-monophosphatedetails
Deoxyuridine triphosphate + Cytidine → dUDP + Cytidine monophosphatedetails
General function:
Involved in oxidoreductase activity
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.
Gene Name:
RRM2B
Uniprot ID:
Q7LG56
Molecular weight:
48786.6

Only showing the first 10 proteins. There are 12 proteins in total.