IMPPAT Phytochemical information: 
4-CDP-2-C-methyl-D-erythritol

4-CDP-2-C-methyl-D-erythritol
Summary

SMILES: OC[C@@]([C@@H](COP(=O)(OP(=O)(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1ccc(nc1=O)N)O)O)O)(O)C
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
InChIKey: YFAUKWZNPVBCFF-XHIBXCGHSA-N
DeepSMILES: OC[C@@][C@@H]COP=O)OP=O)OC[C@H]O[C@H][C@@H][C@@H]5O))O))ncccnc6=O)))N))))))))))O)))O))))O))O)C
Scaffold Graph/Node/Bond level: O=c1ncccn1C1CCCO1
Scaffold Graph/Node level: OC1NCCCN1C1CCCO1
Scaffold Graph level: CC1CCCCC1C1CCCC1
Functional groups: CO; COC; COP(=O)(O)OP(=O)(O)OC; c=O; cN; cn(c)C; cnc
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Nucleosides, nucleotides, and analogues
ClassyFire Class: Pyrimidine nucleotides
ClassyFire Subclass: Pyrimidine ribonucleotides
NP Classifier Biosynthetic pathway: Carbohydrates
NP Classifier Superclass: Aminosugars and aminoglycosides
NP Classifier Class: Aminosugars
Synonymous chemical names:
4-cytidine 5-diphospho-2-c-methyl-d-erythritol
External chemical identifiers:
CID:443199; ChEMBL:CHEMBL1231708; ChEBI:16578; ZINC:ZINC000008419042; SureChEMBL:SCHEMBL254288
Chemical structure download


4-CDP-2-C-methyl-D-erythritol
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 521.31
Log P RDKit -3.2
Topological polar surface area (Å2) RDKit 273.58
Number of hydrogen bond acceptors RDKit 15
Number of hydrogen bond donors RDKit 8
Number of carbon atoms RDKit 14
Number of heavy atoms RDKit 33
Number of heteroatoms RDKit 19
Number of nitrogen atoms RDKit 3
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 6
Stereochemical complexity RDKit 0.43
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 4
Number of sp3 hybridized carbon atoms RDKit 10
Shape complexity RDKit 0.71
Number of rotatable bonds RDKit 11
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 1
Number of aliphatic rings RDKit 1
Number of aromatic carbocycles RDKit 0
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 1
Total number of rings RDKit 2
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 1
Number of saturated rings RDKit 1
Number of Smallest Set of Smallest Rings (SSSR) RDKit 2


4-CDP-2-C-methyl-D-erythritol
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 3
Lipinski’s rule of 5 filter RDKit Failed
Number of Ghose filter violations RDKit 2
Ghose filter RDKit Failed
Veber filter RDKit Bad
Pfizer 3/75 filter RDKit Good
GSK 4/400 filter RDKit Bad
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.1331


4-CDP-2-C-methyl-D-erythritol
ADMET properties
Property nameToolProperty value
Bioavailability score SwissADME 0.11
Solubility class [ESOL] SwissADME Highly soluble
Solubility class [Silicos-IT] SwissADME Soluble
Blood Brain Barrier permeation SwissADME No
Gastrointestinal absorption SwissADME Low
Log Kp (Skin permeation, cm/s) SwissADME -13.53
Number of PAINS structural alerts SwissADME 0.0
Number of Brenk structural alerts SwissADME 1.0
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME No


4-CDP-2-C-methyl-D-erythritol
Predicted human target proteins
Protein identifierHGNC symbolCombined score from STITCH database
ENSP00000385478ISPD871
The human target proteins were predicted using STITCH, a database of Chemical-Protein interaction networks.