Cytidine-5'-Diphosphate

Identification

Generic Name: Cytidine-5'-Diphosphate
DrugBank Accession Number: DB04555
Background: Cytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate. [PubChem]
Type: Small Molecule
Groups: Experimental
Structure: 3D
MOL SDF 3D-SDF PDB SMILES InChI
Similar Structures
Structure for Cytidine-5'-Diphosphate (DB04555)
Synonyms: Not Available

Pharmacology

Indication

Not Available

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Contraindications & Blackbox Warnings

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Pharmacodynamics

Not Available

Mechanism of action

Target	Actions	Organism
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Not Available	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UN-acylneuraminate cytidylyltransferase	Not Available	Neisseria meningitidis
UCytidylate kinase	Not Available	Escherichia coli (strain K12)
UCDP-paratose 2-epimerase	Not Available	Salmonella typhi
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Not Available	Shigella flexneri
U3-deoxy-manno-octulosonate cytidylyltransferase	Not Available	Escherichia coli

Absorption

Not Available

Volume of distribution

Not Available

Protein binding

Not Available

Metabolism

Not Available

Route of elimination

Not Available

Half-life

Not Available

Clearance

Not Available

Adverse Effects

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Toxicity

Not Available

Pathways

Not Available

Pharmacogenomic Effects/ADRs

Not Available

Interactions

Drug Interactions: This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Not Available
Food Interactions: Not Available

Chemical Identifiers

UNII: 1ZH821MXU5
CAS number: 63-38-7
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
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
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

References

General References

Not Available

External Links

Human Metabolome Database: HMDB0001546
KEGG Compound: C00112
PubChem Compound: 6132
PubChem Substance: 46508856
ChemSpider: 5902
BindingDB: 50194153
ChEBI: 17239
ChEMBL: CHEMBL425252
ZINC: ZINC000008215624
PDBe Ligand: CDP

PDB Entries

1eyr / 1ffu / 1gx1 / 1h7h / 1iv2 / 1orr / 1u3l / 1xjn / 1yqn / 2az3 …

show 51 more

Clinical Trials

Clinical Trials

Phase	Status	Purpose	Conditions	Count

Pharmacoeconomics

Manufacturers: Not Available
Packagers: Not Available
Dosage Forms: Not Available
Prices: Not Available
Patents: Not Available

Properties

State

Solid

Experimental Properties

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	10.1 mg/mL	ALOGPS
logP	-1.4	ALOGPS
logP	-3.6	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	-0.52	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	221.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	76.29 m³·mol^-1	ChemAxon
Polarizability	31.39 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted ADMET Features

Property	Value	Probability
Human Intestinal Absorption	-	0.8988
Blood Brain Barrier	+	0.9126
Caco-2 permeable	-	0.7763
P-glycoprotein substrate	Non-substrate	0.7622
P-glycoprotein inhibitor I	Non-inhibitor	0.9175
P-glycoprotein inhibitor II	Non-inhibitor	0.9806
Renal organic cation transporter	Non-inhibitor	0.96
CYP450 2C9 substrate	Non-substrate	0.7402
CYP450 2D6 substrate	Non-substrate	0.8462
CYP450 3A4 substrate	Non-substrate	0.596
CYP450 1A2 substrate	Non-inhibitor	0.9167
CYP450 2C9 inhibitor	Non-inhibitor	0.9233
CYP450 2D6 inhibitor	Non-inhibitor	0.9134
CYP450 2C19 inhibitor	Non-inhibitor	0.9043
CYP450 3A4 inhibitor	Non-inhibitor	0.9438
CYP450 inhibitory promiscuity	Low CYP Inhibitory Promiscuity	0.974
Ames test	Non AMES toxic	0.9125
Carcinogenicity	Non-carcinogens	0.9062
Biodegradation	Not ready biodegradable	0.7826
Rat acute toxicity	2.2404 LD50, mol/kg	Not applicable
hERG inhibition (predictor I)	Weak inhibitor	0.9834
hERG inhibition (predictor II)	Non-inhibitor	0.8137

ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)

Not Available

Spectra

Spectrum	Spectrum Type	Splash Key
Predicted GC-MS Spectrum - GC-MS	Predicted GC-MS	Not Available
Predicted MS/MS Spectrum - 10V, Positive (Annotated)	Predicted LC-MS/MS	splash10-03di-0901000000-6aed044cc4135aa261df
Predicted MS/MS Spectrum - 20V, Positive (Annotated)	Predicted LC-MS/MS	splash10-03di-3900000000-92fac6a8baf47bac3014
Predicted MS/MS Spectrum - 40V, Positive (Annotated)	Predicted LC-MS/MS	splash10-03di-5900000000-5ad7bca4dc732a0e3840
Predicted MS/MS Spectrum - 10V, Negative (Annotated)	Predicted LC-MS/MS	splash10-0a4i-0903300000-44d24cfda26f8f0a8d96
Predicted MS/MS Spectrum - 20V, Negative (Annotated)	Predicted LC-MS/MS	splash10-004i-9701000000-d96a23308bcfcf9cf55f
Predicted MS/MS Spectrum - 40V, Negative (Annotated)	Predicted LC-MS/MS	splash10-004i-9100000000-d7e0d2a5e8d20180b483
LC-MS/MS Spectrum - LC-ESI-ITFT , negative	LC-MS/MS	splash10-004i-9000000000-f5d958a3ccf576052a6b
LC-MS/MS Spectrum - LC-ESI-ITFT , negative	LC-MS/MS	splash10-00di-0390000000-0274cdf4190792442001
LC-MS/MS Spectrum - LC-ESI-ITFT , negative	LC-MS/MS	splash10-0udi-0009000000-2c8a9272dc29076a6167
LC-MS/MS Spectrum - LC-ESI-QTOF , negative	LC-MS/MS	splash10-0kdi-9602700000-4b46ddc9506634a02dc5
LC-MS/MS Spectrum - LC-ESI-ITFT , positive	LC-MS/MS	splash10-0a4i-0059000000-d598d99a604dda402181
LC-MS/MS Spectrum - LC-ESI-QTOF , positive	LC-MS/MS	splash10-0udi-0003900000-69398917fb0c37a4304f
LC-MS/MS Spectrum - LC-ESI-QTOF , positive	LC-MS/MS	splash10-0zg0-0726900000-8d967e8ca6677a467fb8
1H NMR Spectrum	1D NMR	Not Applicable
13C NMR Spectrum	1D NMR	Not Applicable

Targets

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Details1. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Kind: Protein
Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Pharmacological action: Unknown

General Function: Metal ion binding
Specific Function: Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidy...
Gene Name: ispF
Uniprot ID: Q8RQP5
Uniprot Name: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular Weight: 16519.835 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Details2. N-acylneuraminate cytidylyltransferase

Kind: Protein
Organism: Neisseria meningitidis
Pharmacological action: Unknown

General Function: N-acylneuraminate cytidylyltransferase activity
Specific Function: Not Available
Gene Name: neuA
Uniprot ID: P0A0Z8
Uniprot Name: N-acylneuraminate cytidylyltransferase
Molecular Weight: 24892.155 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Details3. Cytidylate kinase

Kind: Protein
Organism: Escherichia coli (strain K12)
Pharmacological action: Unknown

General Function: 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
Uniprot Name: Cytidylate kinase
Molecular Weight: 24746.03 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Details4. CDP-paratose 2-epimerase

Kind: Protein
Organism: Salmonella typhi
Pharmacological action: Unknown

General Function: Cdp-abequose epimerase activity
Specific Function: Catalyzes the isomeration of CDP-paratose to CDP-tyvelose.
Gene Name: rfbE
Uniprot ID: P14169
Uniprot Name: CDP-paratose 2-epimerase
Molecular Weight: 37957.675 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Details5. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Kind: Protein
Organism: Shigella flexneri
Pharmacological action: Unknown

General Function: Metal ion binding
Specific Function: Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidy...
Gene Name: ispF
Uniprot ID: P62619
Uniprot Name: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular Weight: 16897.37 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Details6. 3-deoxy-manno-octulosonate cytidylyltransferase

Kind: Protein
Organism: Escherichia coli
Pharmacological action: Unknown

General Function: 3-deoxy-manno-octulosonate cytidylyltransferase activity
Specific Function: Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
Gene Name: kpsU
Uniprot ID: P42216
Uniprot Name: 3-deoxy-manno-octulosonate cytidylyltransferase
Molecular Weight: 27158.885 Da

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Drug created on June 13, 2005 13:24 / Updated on June 12, 2020 16:52

Cytidine-5'-Diphosphate

Identification

Structure for Cytidine-5'-Diphosphate (DB04555)

Pharmacology

Interactions

Categories

Chemical Identifiers

References

Clinical Trials

Pharmacoeconomics

Properties

Spectra

Targets

References

References

References

References

References

References