NAV

4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol

Identification

Generic Name
4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
DrugBank Accession Number
DB03687
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 521.3075
Monoisotopic: 521.081175547
Chemical Formula
C14H25N3O14P2
Synonyms
  • 4-CDP-2-C-methyl-D-erythritol
  • 4-Diphosphocytidyl-2-C-methyl-D-erythritol
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseNot AvailableShigella flexneri
U4-diphosphocytidyl-2-C-methyl-D-erythritol kinaseNot AvailableShigella flexneri
U2-C-methyl-D-erythritol 4-phosphate cytidylyltransferaseNot AvailableEscherichia coli (strain K12)
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 / Monosaccharide phosphates / Organic pyrophosphates / Aminopyrimidines and derivatives / Monoalkyl phosphates / Pyrimidones / Hydropyrimidines / Imidolactams / Tetrahydrofurans
show 11 more
Substituents
Alcohol / Alkyl phosphate / Amine / Aminopyrimidine / Aromatic heteromonocyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine
show 28 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
alditol 4-phosphate, tetritol phosphate, nucleotide-alditol (CHEBI:16578)
Affected organisms
Not Available

Chemical Identifiers

UNII
FB44VKC5JD
CAS number
263016-94-0
InChI Key
YFAUKWZNPVBCFF-XHIBXCGHSA-N
InChI
InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1
IUPAC Name
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphoryl}oxy)phosphinic acid
SMILES
C[C@](O)(CO)[C@H](O)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O

References

General References
Not Available
KEGG Compound
C11435
PubChem Compound
443199
PubChem Substance
46508868
ChemSpider
391471
ChEBI
16578
ChEMBL
CHEMBL1231708
ZINC
ZINC000008419042
PDBe Ligand
CDM
PDB Entries
1ini / 1oj4 / 1u40 / 2v2z / 3pye / 3q80

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
logP-3.9Chemaxon
pKa (Strongest Acidic)1.84Chemaxon
pKa (Strongest Basic)3.56Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count14Chemaxon
Hydrogen Donor Count9Chemaxon
Polar Surface Area272.35 Å2Chemaxon
Rotatable Bond Count11Chemaxon
Refractivity115.04 m3·mol-1Chemaxon
Polarizability44.23 Å3Chemaxon
Number of Rings2Chemaxon
Bioavailability0Chemaxon
Rule of FiveNoChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption+0.6071
Blood Brain Barrier+0.7006
Caco-2 permeable-0.7175
P-glycoprotein substrateSubstrate0.5456
P-glycoprotein inhibitor INon-inhibitor0.8692
P-glycoprotein inhibitor IINon-inhibitor0.9936
Renal organic cation transporterNon-inhibitor0.9762
CYP450 2C9 substrateNon-substrate0.7196
CYP450 2D6 substrateNon-substrate0.8283
CYP450 3A4 substrateNon-substrate0.554
CYP450 1A2 substrateNon-inhibitor0.8618
CYP450 2C9 inhibitorNon-inhibitor0.8617
CYP450 2D6 inhibitorNon-inhibitor0.866
CYP450 2C19 inhibitorNon-inhibitor0.8366
CYP450 3A4 inhibitorNon-inhibitor0.9137
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9658
Ames testNon AMES toxic0.7107
CarcinogenicityNon-carcinogens0.8258
BiodegradationNot ready biodegradable0.9652
Rat acute toxicity2.3188 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9623
hERG inhibition (predictor II)Non-inhibitor0.7904
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 MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-000i-0000940000-d9b56d79952b60a35237
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-00di-0000090000-6e34a52523b53d2d846a
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0fi0-0379420000-d0ce230a7dbce44ecd9d
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-00fr-2301930000-b3d22c3d855d677eef8b
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-00dj-7339110000-cfc524c860f70cc67363
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-002b-9414410000-289c6dbf199f0d962974
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-214.6289813
predicted
DarkChem Lite v0.1.0
[M-H]-188.76128
predicted
DeepCCS 1.0 (2019)
[M+H]+214.8925813
predicted
DarkChem Lite v0.1.0
[M+H]+190.70747
predicted
DeepCCS 1.0 (2019)
[M+Na]+213.9020813
predicted
DarkChem Lite v0.1.0
[M+Na]+196.62047
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. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Kind
Protein
Organism
Shigella flexneri
Pharmacological action
Unknown
General Function
Atp binding
Specific Function
Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol.
Gene Name
ispE
Uniprot ID
Q83LD8
Uniprot Name
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Molecular Weight
30953.11 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 4-phosphate cytidylyltransferase
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Magnesium ion binding
Specific Function
Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).
Gene Name
ispD
Uniprot ID
Q46893
Uniprot Name
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Molecular Weight
25736.995 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