Human Metabolome Database Version 3.5

Showing metabocard for CDP (HMDB01546)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:10:45 -0700
HMDB ID HMDB01546
Secondary Accession Numbers None
Metabolite Identification
Common Name CDP
Description Cytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate.
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. CDP
  2. Cytidine-5'-diphosphate
  3. Cytidine-diphosphate
Chemical Formula C9H15N3O11P2
Average Molecular Weight 403.1764
Monoisotopic Molecular Weight 403.018181361
IUPAC Name [({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name {[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry Number 63-38-7
SMILES NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChI Key ZWIADYZPOWUWEW-XVFCMESISA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleotides
Sub Class Pyrimidine Ribonucleotides
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Ribonucleotides(KEGG)
  • cytidine 5'-phosphate(ChEBI)
  • pyrimidine ribonucleoside 5'-diphosphate(ChEBI)
Substituents
  • 1,2 Diol
  • Aminopyrimidine
  • Glycosyl Compound
  • Hydropyrimidine
  • Monosaccharide Phosphate
  • N Glycosyl Compound
  • Organic Hypophosphite
  • Organic Phosphite
  • Organic Pyrophosphate
  • Oxolane
  • Pentose Monosaccharide
  • Phosphoric Acid Ester
  • Pyrimidine
  • Pyrimidone
  • Saccharide
  • Secondary Alcohol
Direct Parent Pyrimidine Ribonucleoside Diphosphates
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Mitochondria
  • Nucleus
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP 2.44 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 10.1 g/L ALOGPS
LogP -1.38 ALOGPS
LogP -3.6 ChemAxon
LogS -1.60 ALOGPS
pKa (strongest acidic) 1.77 ChemAxon
pKa (strongest basic) -0.52 ChemAxon
Hydrogen Acceptor Count 11 ChemAxon
Hydrogen Donor Count 6 ChemAxon
Polar Surface Area 221.67 A2 ChemAxon
Rotatable Bond Count 6 ChemAxon
Refractivity 76.29 ChemAxon
Polarizability 31.39 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -2 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
Tissue Location Not Available
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
36.0 +/- 12.0 uM Adult (>18 years old) Both Normal
  • Geigy Scient...
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB022683
KNApSAcK ID Not Available
Chemspider ID 5902 Link_out
KEGG Compound ID C00112 Link_out
BioCyc ID CDP Link_out
BiGG ID 33901 Link_out
Wikipedia Link CDP Link_out
NuGOwiki Link HMDB01546 Link_out
Metagene Link HMDB01546 Link_out
METLIN ID 6313 Link_out
PubChem Compound 6132 Link_out
PDB ID CDP Link_out
ChEBI ID 17239 Link_out
References
Synthesis Reference Chambers, Robert Warner; Shapiro, Philip; Kurkov, Viktor. Synthesis of cytidine 5'-diphosphate and guanosine 5'-diphosphate. Journal of the American Chemical Society (1960), 82 970-5.
Material Safety Data Sheet (MSDS) Not Available
General References
  1. George TP, Cook HW, Byers DM, Palmer FB, Spence MW: Inhibition of phosphatidylcholine and phosphatidylethanolamine biosynthesis by cytochalasin B in cultured glioma cells: potential regulation of biosynthesis by Ca(2+)-dependent mechanisms. Biochim Biophys Acta. 1991 Jul 9;1084(2):185-93. Pubmed: 1854804 Link_out
  2. Riekhof WR, Voelker DR: Uptake and utilization of lyso-phosphatidylethanolamine by Saccharomyces cerevisiae. J Biol Chem. 2006 Dec 1;281(48):36588-96. Epub 2006 Oct 2. Pubmed: 17015438 Link_out
  3. Tsitolovskii LE, Kraevskii AA: [Possible relation between learning and non-template RNA synthesis in neurons]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1982 Mar-Apr;32(2):284-91. Pubmed: 6178232 Link_out
  4. Houtkooper RH, Akbari H, van Lenthe H, Kulik W, Wanders RJ, Frentzen M, Vaz FM: Identification and characterization of human cardiolipin synthase. FEBS Lett. 2006 May 29;580(13):3059-64. Epub 2006 Apr 27. Pubmed: 16678169 Link_out
  5. Carstensen S, Pliska-Matyshak G, Bhuvarahamurthy N, Robbins KM, Murthy PP: Biosynthesis and localization of phosphatidyl-scyllo-inositol in barley aleurone cells. Lipids. 1999 Jan;34(1):67-73. Pubmed: 10188599 Link_out
  6. Nowicki M, Muller F, Frentzen M: Cardiolipin synthase of Arabidopsis thaliana. FEBS Lett. 2005 Apr 11;579(10):2161-5. Pubmed: 15811335 Link_out
  7. George TP, Morash SC, Cook HW, Byers DM, Palmer FB, Spence MW: Phosphatidylcholine biosynthesis in cultured glioma cells: evidence for channeling of intermediates. Biochim Biophys Acta. 1989 Aug 22;1004(3):283-91. Pubmed: 2758024 Link_out
  8. Houtkooper RH, Vaz FM: Cardiolipin, the heart of mitochondrial metabolism. Cell Mol Life Sci. 2008 Aug;65(16):2493-506. doi: 10.1007/s00018-008-8030-5. Pubmed: 18425414 Link_out
  9. Lindblad L, Schersten T: Incorporation rate in vitro of choline and methyl-methionine into human hepatic lecithins. Scand J Gastroenterol. 1976;11(6):587-91. Pubmed: 981963 Link_out

Enzymes
Name: UMP-CMP kinase
Reactions:
Adenosine triphosphate + Cytidine monophosphate unknown ADP + CDP details
Gene Name: CMPK1
Uniprot ID: P30085 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 1
Reactions:
CDP + Water unknown Cytidine monophosphate + Phosphoric acid details
Cytidine triphosphate + Water unknown CDP + Phosphoric acid details
Gene Name: ENTPD1
Uniprot ID: P49961 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Soluble calcium-activated nucleotidase 1
Reactions: Not Available
Gene Name: CANT1
Uniprot ID: Q8WVQ1 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 3
Reactions:
CDP + Water unknown Cytidine monophosphate + Phosphoric acid details
Cytidine triphosphate + Water unknown CDP + Phosphoric acid details
Gene Name: ENTPD3
Uniprot ID: O75355 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase, mitochondrial
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME4
Uniprot ID: O00746 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ribonucleoside-diphosphate reductase large subunit
Reactions:
dCDP + Thioredoxin disulfide + Water unknown Thioredoxin + CDP details
Gene Name: RRM1
Uniprot ID: P23921 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase A
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME1
Uniprot ID: P15531 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase 7
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME7
Uniprot ID: Q9Y5B8 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ribonucleoside-diphosphate reductase subunit M2
Reactions:
dCDP + Thioredoxin disulfide + Water unknown Thioredoxin + CDP details
Gene Name: RRM2
Uniprot ID: P31350 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase B
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME2
Uniprot ID: P22392 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase 3
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME3
Uniprot ID: Q13232 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase 6
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME6
Uniprot ID: O75414 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 6-phosphofructokinase type C
Reactions:
Cytidine triphosphate + D-Tagatose 6-phosphate unknown CDP + D-Tagatose 1,6-bisphosphate details
Gene Name: PFKP
Uniprot ID: Q01813 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 6-phosphofructokinase, liver type
Reactions:
Cytidine triphosphate + D-Tagatose 6-phosphate unknown CDP + D-Tagatose 1,6-bisphosphate details
Gene Name: PFKL
Uniprot ID: P17858 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 6-phosphofructokinase, muscle type
Reactions:
Cytidine triphosphate + D-Tagatose 6-phosphate unknown CDP + D-Tagatose 1,6-bisphosphate details
Gene Name: PFKM
Uniprot ID: P08237 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Pyruvate kinase isozymes M1/M2
Reactions: Not Available
Gene Name: PKM
Uniprot ID: P14618 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Pyruvate kinase isozymes R/L
Reactions: Not Available
Gene Name: PKLR
Uniprot ID: P30613 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 4
Reactions: Not Available
Gene Name: ENTPD4
Uniprot ID: Q9Y227 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 6
Reactions: Not Available
Gene Name: ENTPD6
Uniprot ID: O75354 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 5
Reactions: Not Available
Gene Name: ENTPD5
Uniprot ID: O75356 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
Reactions:
RNA + Phosphoric acid unknown RNA + CDP details
Gene Name: PNPT1
Uniprot ID: Q8TCS8 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ribonucleoside-diphosphate reductase subunit M2 B
Reactions:
dCDP + Thioredoxin disulfide + Water unknown Thioredoxin + CDP details
Gene Name: RRM2B
Uniprot ID: Q7LG56 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UMP-CMP kinase 2, mitochondrial
Reactions:
Adenosine triphosphate + Cytidine monophosphate unknown ADP + CDP details
Gene Name: CMPK2
Uniprot ID: Q5EBM0 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 8
Reactions:
CDP + Water unknown Cytidine monophosphate + Phosphoric acid details
Cytidine triphosphate + Water unknown CDP + Phosphoric acid details
Gene Name: ENTPD8
Uniprot ID: Q5MY95 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Putative nucleoside diphosphate kinase
Reactions: Not Available
Gene Name: NME2P1
Uniprot ID: O60361 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Probable 8-oxo-dGTP diphosphatase NUDT15
Reactions: Not Available
Gene Name: NUDT15
Uniprot ID: Q9NV35 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate-linked moiety X motif 17
Reactions: Not Available
Gene Name: NUDT17
Uniprot ID: P0C025 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 8-oxo-dGDP phosphatase NUDT18
Reactions: Not Available
Gene Name: NUDT18
Uniprot ID: Q6ZVK8 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate-linked moiety X motif 8, mitochondrial
Reactions: Not Available
Gene Name: NUDT8
Uniprot ID: Q8WV74 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Dolichol kinase
Reactions:
Cytidine triphosphate + dolichol unknown CDP + Dolichol-20 details
Gene Name: DOLK
Uniprot ID: Q9UPQ8 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase
Reactions: Not Available
Gene Name: NME4
Uniprot ID: A2IDD0 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase homolog 5
Reactions:
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphate details
Gene Name: NME5
Uniprot ID: P56597 Link_out