PDB Entry (6fdq) |
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PDB ID: 6fdq | Resolution: 2.3 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 30028574 | DOI: 10.1002/cmdc.201800364 | |
Protein |
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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 |
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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 |
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Database Name | Value |
PDBBind | IC50 : 113000 nM |