CDP (ECMDB01546) (M2MDB000415)
Record Information | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Version | 2.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Creation Date | 2012-05-31 13:54:15 -0600 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Update Date | 2015-06-03 15:54:11 -0600 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Secondary Accession Numbers |
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Identification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Name: | CDP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Description | Cytidine 5'-(trihydrogen diphosphate) is cytosine nucleotide containing two phosphate groups esterified to the sugar (ribose) moiety. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Synonyms: |
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Chemical Formula: | C9H15N3O11P2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Weight: | Average: 403.1764 Monoisotopic: 403.018181361 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
InChI Key: | ZWIADYZPOWUWEW-XVFCMESISA-N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
InChI: | 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CAS number: | 63-38-7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: | CDP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Chemical Taxonomy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Description | belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Kingdom | Organic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Super Class | Nucleosides, nucleotides, and analogues | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Class | Pyrimidine nucleotides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sub Class | Pyrimidine ribonucleotides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Direct Parent | Pyrimidine ribonucleoside diphosphates | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Alternative Parents |
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Substituents |
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Molecular Framework | Aromatic heteromonocyclic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
External Descriptors |
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Physical Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
State: | Solid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Charge: | -2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Melting point: | Not Available | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Experimental Properties: |
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Predicted Properties |
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Biological Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cellular Locations: | Cytoplasm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reactions: | CDP + Reduced Thioredoxin > dCDP + Water + Oxidized Thioredoxin CDP + glutaredoxin > dCDP + glutaredoxin + Water Adenosine triphosphate + CDP <> ADP + Cytidine triphosphate Adenosine triphosphate + Cytidine monophosphate <> ADP + CDP Cytidine triphosphate + Water > CDP + Hydrogen ion + Phosphate RNA + Phosphate <> RNA + CDP dCDP + Thioredoxin disulfide + Water <> Thioredoxin + CDP Cytidine triphosphate + D-Tagatose 6-phosphate <> CDP + D-Tagatose 1,6-bisphosphate CDP + Adenosine triphosphate > Cytidine triphosphate + ADP CDP + Water > Phosphate + Cytidine monophosphate + Hydrogen ion CDP + a reduced NrdH glutaredoxin-like protein > Water + dCDP + an oxidized NrdH glutaredoxin-like protein CDP + reduced thioredoxin > Water + oxidized thioredoxin + dCDP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMPDB Pathways: |
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KEGG Pathways: |
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EcoCyc Pathways: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Concentrations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Find out more about how we convert literature concentrations. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spectra | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spectra: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
References: |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Links | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
External Links: |
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Enzymes
- General function:
- Involved in oxidation-reduction process
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
- Gene Name:
- nrdA
- Uniprot ID:
- P00452
- Molecular weight:
- 85774
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in RNA binding
- Specific function:
- Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction
- Gene Name:
- pnp
- Uniprot ID:
- P05055
- Molecular weight:
- 77100
Reactions
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate. |
- General function:
- Involved in phosphotransferase activity, alcohol group as acceptor
- Specific function:
- ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate
- Gene Name:
- pfkB
- Uniprot ID:
- P06999
- Molecular weight:
- 32456
Reactions
ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate. |
- General function:
- Involved in cytidylate kinase activity
- Specific function:
- ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors
- Gene Name:
- cmk
- Uniprot ID:
- P0A6I0
- Molecular weight:
- 24746
Reactions
ATP + (d)CMP = ADP + (d)CDP. |
- 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:
- ndk
- Uniprot ID:
- P0A763
- Molecular weight:
- 15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. |
- General function:
- Involved in ATP binding
- Specific function:
- ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate
- Gene Name:
- pfkA
- Uniprot ID:
- P0A796
- Molecular weight:
- 34842
Reactions
ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate. |
- General function:
- Involved in electron carrier activity
- Specific function:
- Efficient electron donor for the essential enzyme ribonucleotide reductase. Is also able to reduce the interchain disulfide bridges of insulin
- Gene Name:
- trxC
- Uniprot ID:
- P0AGG4
- Molecular weight:
- 15555
Reactions
Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H. |
- General function:
- Involved in oxidoreductase activity
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F contains the tyrosyl radical required for catalysis
- Gene Name:
- nrdF
- Uniprot ID:
- P37146
- Molecular weight:
- 36443
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in GTPase activity
- Specific function:
- May play a role in 30S ribosomal subunit biogenesis. Unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. Dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes (PubMed:14973029). The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin (PubMed:15466596) streptomycin and spectinomycin (PubMed:15828870). This inhibition is not due to competition for binding sites on the 30S or 70S ribosome (PubMed:15828870)
- Gene Name:
- rsgA
- Uniprot ID:
- P39286
- Molecular weight:
- 39193
- General function:
- Involved in oxidation-reduction process
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide
- Gene Name:
- nrdE
- Uniprot ID:
- P39452
- Molecular weight:
- 80478
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in ATP binding
- Specific function:
- Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
- Gene Name:
- adk
- Uniprot ID:
- P69441
- Molecular weight:
- 23586
Reactions
ATP + AMP = 2 ADP. |
- General function:
- Involved in oxidoreductase activity
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
- Gene Name:
- nrdB
- Uniprot ID:
- P69924
- Molecular weight:
- 43517
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in electron carrier activity
- Specific function:
- Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
- Gene Name:
- grxD
- Uniprot ID:
- P0AC69
- Molecular weight:
- 12879
- General function:
- Involved in electron carrier activity
- Specific function:
- The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
- Gene Name:
- grxC
- Uniprot ID:
- P0AC62
- Molecular weight:
- 9137
- General function:
- Involved in protein binding
- Specific function:
- Involved in reducing some disulfides in a coupled system with glutathione reductase. Does not act as hydrogen donor for ribonucleotide reductase
- Gene Name:
- grxB
- Uniprot ID:
- P0AC59
- Molecular weight:
- 24350
- General function:
- Involved in electron carrier activity
- Specific function:
- The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
- Gene Name:
- grxA
- Uniprot ID:
- P68688
- Molecular weight:
- 9685
- General function:
- Involved in electron carrier activity
- Specific function:
- Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions
- Gene Name:
- trxA
- Uniprot ID:
- P0AA25
- Molecular weight:
- 11807
Transporters
- 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:
- ndk
- Uniprot ID:
- P0A763
- Molecular weight:
- 15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. |