PDB Entry (6fdu) |
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PDB ID: 6fdu | 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: (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 |
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Database Name | Value |
PDBBind | IC50 : 204000 nM |