NAV

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
Similar Structures
Weight
Average: 403.1764
Monoisotopic: 403.018181361
Chemical Formula
C9H15N3O11P2
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Contraindications & Blackbox Warnings
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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseNot AvailableShigella flexneri
U3-deoxy-manno-octulosonate cytidylyltransferaseNot AvailableEscherichia coli
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseNot AvailableThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UN-acylneuraminate cytidylyltransferaseNot AvailableNeisseria meningitidis
UCytidylate kinaseNot AvailableEscherichia coli (strain K12)
UCDP-paratose 2-epimeraseNot AvailableSalmonella typhi
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

Categories

Drug Categories
Not Available
Chemical TaxonomyProvided by Classyfire
Description
This compound 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
Pentose phosphates / Glycosylamines / Organic pyrophosphates / Monosaccharide phosphates / Aminopyrimidines and derivatives / Pyrimidones / Monoalkyl phosphates / Hydropyrimidines / Imidolactams / Tetrahydrofurans
show 9 more
Substituents
1,2-diol / Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative
show 26 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
cytidine 5'-phosphate, pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17239) / Ribonucleotides (C00112)
Affected organisms
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
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 53 more

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount

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
PropertyValueSource
Water Solubility10.1 mg/mLALOGPS
logP-1.4ALOGPS
logP-3.5Chemaxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.74Chemaxon
pKa (Strongest Basic)4.33Chemaxon
Physiological Charge-3Chemaxon
Hydrogen Acceptor Count11Chemaxon
Hydrogen Donor Count6Chemaxon
Polar Surface Area221.67 Å2Chemaxon
Rotatable Bond Count6Chemaxon
Refractivity76.29 m3·mol-1Chemaxon
Polarizability31.39 Å3Chemaxon
Number of Rings2Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.8988
Blood Brain Barrier+0.9126
Caco-2 permeable-0.7763
P-glycoprotein substrateNon-substrate0.7622
P-glycoprotein inhibitor INon-inhibitor0.9175
P-glycoprotein inhibitor IINon-inhibitor0.9806
Renal organic cation transporterNon-inhibitor0.96
CYP450 2C9 substrateNon-substrate0.7402
CYP450 2D6 substrateNon-substrate0.8462
CYP450 3A4 substrateNon-substrate0.596
CYP450 1A2 substrateNon-inhibitor0.9167
CYP450 2C9 inhibitorNon-inhibitor0.9233
CYP450 2D6 inhibitorNon-inhibitor0.9134
CYP450 2C19 inhibitorNon-inhibitor0.9043
CYP450 3A4 inhibitorNon-inhibitor0.9438
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.974
Ames testNon AMES toxic0.9125
CarcinogenicityNon-carcinogens0.9062
BiodegradationNot ready biodegradable0.7826
Rat acute toxicity2.2404 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9834
hERG inhibition (predictor II)Non-inhibitor0.8137
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSsplash10-004i-5923000000-f7e7b227d8dab9e29e4b
LC-MS/MS Spectrum - LC-ESI-ITFT , negativeLC-MS/MSsplash10-004i-9000000000-f5d958a3ccf576052a6b
LC-MS/MS Spectrum - LC-ESI-ITFT , negativeLC-MS/MSsplash10-00di-0390000000-0274cdf4190792442001
LC-MS/MS Spectrum - LC-ESI-ITFT , negativeLC-MS/MSsplash10-0udi-0009000000-2c8a9272dc29076a6167
LC-MS/MS Spectrum - LC-ESI-QTOF , negativeLC-MS/MSsplash10-0kdi-9602700000-4b46ddc9506634a02dc5
LC-MS/MS Spectrum - LC-ESI-ITFT , positiveLC-MS/MSsplash10-0a4i-0059000000-d598d99a604dda402181
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-0udi-0003900000-69398917fb0c37a4304f
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-0zg0-0726900000-8d967e8ca6677a467fb8
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0udi-0300900000-b6b189a9739a2fabadfc
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0udi-0001900000-58183fd7eda9654648a6
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-0910000000-dd10d617cc2a5fbfc22e
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-056r-9107000000-0943f4a1d4895da4dd60
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-2900000000-7dd70dc1e6b4e964a068
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9000000000-0d4f5207647e0c0c6d7e
1H NMR Spectrum1D NMRNot Applicable
13C NMR Spectrum1D NMRNot Applicable
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-197.7552258
predicted
DarkChem Lite v0.1.0
[M-H]-162.31212
predicted
DeepCCS 1.0 (2019)
[M+H]+199.4477258
predicted
DarkChem Lite v0.1.0
[M+H]+164.77
predicted
DeepCCS 1.0 (2019)
[M+Na]+199.8174258
predicted
DarkChem Lite v0.1.0
[M+Na]+172.35509
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. 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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. 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. 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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. 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. 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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. 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. 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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. 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. 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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. 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. 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
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. 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 at June 13, 2005 13:24 / Updated at June 12, 2020 16:52