PDB Entry (6fdq)
PDB ID: 6fdq Resolution: 2.3 Å Exp. Method: X-RAY DIFFRACTION
PMID: 30028574 DOI: 10.1002/cmdc.201800364
Protein
Protein Name: Deubiquitinase and deneddylase Dub1
Uniprot ID/ACC: B0B9A0 (CDUB1_CHLT2) Organism: Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B)
Gene Symbol: cdu1 Gene ID: -
Protein Class: HYDROLASE
Ligand
Ligand Name:   N-benzyl-2-cyanopyrimidine-5-carboxamide
Canonical SMILES:   N#Cc1ncc(cn1)C(=O)NCc2ccccc2
Standard InChI:   InChI=1S/C13H10N4O/c14-6-12-15-8-11(9-16-12)13(18)17-7-10-4-2-1-3-5-10/h1-5,8-9H,7H2,(H,17,18)
HET Code:   2UQ PubChem:   118711629
DrugBank:   - ChEMBL:   CHEMBL3326421
Molecular Formula:   C13H10N4O Mol. Weight:   238.08546 logP:   1.27828
HBD:   1 HBA:   4
#Rotatable Bonds:   3 TPSA:   78.67
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Addition to a Triple Bond CYS 345 A 14.73 13.41 Nitrile
Binding Affinity
Database Name Value
PDBBind IC50 : 113000 nM