Hmp_logo

Human Metabolome Database Version 3.5

HMDB has recently undergone some major changes, if you are experiencing problems please click here to provide us with feedback.

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 | 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 Comments
Blood Detected and Quantified
Article_icon
36.0 +/- 12.0 uM Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank 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 Not Available
Enzymes
Name: Ectonucleoside triphosphate diphosphohydrolase 1
Reactions:
  • ATP + 2 H2O = AMP + 2 phosphate [RN:R00085]
Gene Name: ENTPD1
Uniprot ID: P49961 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Soluble calcium-activated nucleotidase 1
Reactions:
  • a nucleoside diphosphate + H2O = a nucleotide + phosphate [RN:R00329]
Gene Name: CANT1
Uniprot ID: Q8WVQ1 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 3
Reactions:
  • ATP + 2 H2O = AMP + 2 phosphate [RN:R00085]
Gene Name: ENTPD3
Uniprot ID: O75355 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase, mitochondrial
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME4
Uniprot ID: O00746 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ribonucleoside-diphosphate reductase large subunit
Reactions:
  • 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin [RN:R04294]
Gene Name: RRM1
Uniprot ID: P23921 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase A
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME1
Uniprot ID: P15531 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase 7
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME7
Uniprot ID: Q9Y5B8 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ribonucleoside-diphosphate reductase subunit M2
Reactions:
  • 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin [RN:R04294]
Gene Name: RRM2
Uniprot ID: P31350 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase B
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME2
Uniprot ID: P22392 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase 3
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME3
Uniprot ID: Q13232 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Nucleoside diphosphate kinase 6
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME6
Uniprot ID: O75414 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 6-phosphofructokinase type C
Reactions:
  • ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate [RN:R00756]
Gene Name: PFKP
Uniprot ID: Q01813 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 6-phosphofructokinase, liver type
Reactions:
  • ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate [RN:R00756]
Gene Name: PFKL
Uniprot ID: P17858 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 6-phosphofructokinase, muscle type
Reactions:
  • ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate [RN:R00756]
Gene Name: PFKM
Uniprot ID: P08237 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Pyruvate kinase isozymes M1/M2
Reactions:
  • ATP + pyruvate = ADP + phosphoenolpyruvate [RN:R00200]
Gene Name: PKM2
Uniprot ID: P14618 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Pyruvate kinase isozymes R/L
Reactions:
  • ATP + pyruvate = ADP + phosphoenolpyruvate [RN:R00200]
Gene Name: PKLR
Uniprot ID: P30613 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 4
Reactions:
  • a nucleoside diphosphate + H2O = a nucleotide + phosphate [RN:R00329]
Gene Name: ENTPD4
Uniprot ID: Q9Y227 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 6
Reactions:
  • a nucleoside diphosphate + H2O = a nucleotide + phosphate [RN:R00329]
Gene Name: ENTPD6
Uniprot ID: O75354 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 5
Reactions:
  • a nucleoside diphosphate + H2O = a nucleotide + phosphate [RN:R00329]
Gene Name: ENTPD5
Uniprot ID: O75356 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
Reactions:
  • RNAn+1 + phosphate = RNAn + a nucleoside diphosphate [RN:R07282]
Gene Name: PNPT1
Uniprot ID: Q8TCS8 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ribonucleoside-diphosphate reductase subunit M2 B
Reactions:
  • 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin [RN:R04294]
Gene Name: RRM2B
Uniprot ID: Q7LG56 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UMP-CMP kinase 2, mitochondrial
Reactions:
  • ATP + (d)CMP = ADP + (d)CDP [RN:R00512 R01665]
Gene Name: CMPK2
Uniprot ID: Q5EBM0 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 8
Reactions:
  • ATP + 2 H2O = AMP + 2 phosphate [RN:R00085]
Gene Name: ENTPD8
Uniprot ID: Q5MY95 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Putative nucleoside diphosphate kinase
Reactions:
  • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
Gene Name: NME2P1
Uniprot ID: O60361 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Probable 7,8-dihydro-8-oxoguanine triphosphatase NUDT15
Reactions:
    Gene Name: NUDT15
    Uniprot ID: Q9NV35 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Nucleoside diphosphate-linked moiety X motif 17
    Reactions:
      Gene Name: NUDT17
      Uniprot ID: P0C025 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Nucleoside diphosphate-linked moiety X motif 18
      Reactions:
        Gene Name: NUDT18
        Uniprot ID: Q6ZVK8 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Nucleoside diphosphate-linked moiety X motif 8, mitochondrial
        Reactions:
          Gene Name: NUDT8
          Uniprot ID: Q8WV74 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Dolichol kinase
          Reactions:
          • CTP + dolichol = CDP + dolichyl phosphate [RN:R01018]
          Gene Name: DOLK
          Uniprot ID: Q9UPQ8 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Nucleoside diphosphate kinase
          Reactions:
          • ATP + nucleoside diphosphate = ADP + nucleoside triphosphate [RN:R00331]
          Gene Name: NME4
          Uniprot ID: A2IDD0 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA