PDB Entry (6fdu)
PDB ID: 6fdu 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:   (2S,3S)-N-[(2-cyanopyrimidin-4-yl)methyl]-2-[(2S)-2-(3,5-dichlorophenyl)-2-(dimethylamino)acetamido]-3-methylpentanamide
Canonical SMILES:   Clc1cc(cc(Cl)c1)[C@H](N(C)C)C(=O)N[C@@H]([C@@H](C)CC)C(=O)NCc2ccnc(n2)C#N
Standard InChI:   InChI=1S/C22H26Cl2N6O2/c1-5-13(2)19(21(31)27-12-17-6-7-26-18(11-25)28-17)29-22(32)20(30(3)4)14-8-15(23)10-16(24)9-14/h6-10,13,19-20H,5,12H2,1-4H3,(H,27,31)(H,29,32)/t13-,19-,20-/m0/s1
HET Code:   D5W PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C22H26Cl2N6O2 Mol. Weight:   476.14944 logP:   3.10508
HBD:   2 HBA:   6
#Rotatable Bonds:   9 TPSA:   111.01
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Addition to a Triple Bond CYS 345 B 14.51 13.13 Nitrile
Binding Affinity
Database Name Value
PDBBind IC50 : 204000 nM