PDB Entry (6b88)
PDB ID: 6b88 Resolution: 2.41 Å Exp. Method: X-RAY DIFFRACTION
PMID: 30209367 DOI: 10.1038/s41586-018-0483-6
Protein
Protein Name: Signal peptidase I
Uniprot ID/ACC: P00803 (LEP_ECOLI) Organism: Escherichia coli (strain K12)
Gene Symbol: lepB Gene ID: 57732329
Protein Class: HYDROLASE
Ligand
Ligand Name:   GNE0775
Canonical SMILES:   C[C@@H]1NC(=O)[C@@H](N(C)C(=O)[C@H](CCN)NC(=O)c2cnc(nc2C)-c2ccc(cc2)C(C)(C)C)c2ccc(OCCN)c(c2)-c2cc(C[C@H](NC1=O)C(=O)NCC#N)ccc2OCCN
Standard InChI:   InChI=1S/C47H59N11O7/c1-27-35(26-53-41(54-27)30-8-11-32(12-9-30)47(3,4)5)43(60)56-36(15-16-48)46(63)58(6)40-31-10-14-39(65-22-19-51)34(25-31)33-23-29(7-13-38(33)64-21-18-50)24-37(44(61)52-20-17-49)57-42(59)28(2)55-45(40)62/h7-14,23,25-26,28,36-37,40H,15-16,18-22,24,48,50-51H2,1-6H3,(H,52,61)(H,55,62)(H,56,60)(H,57,59)/t28-,36-,37-,40-/m0/s1
HET Code:   CZD PubChem:   134827876
DrugBank:   - ChEMBL:   -
Molecular Formula:   C47H59N11O7 Mol. Weight:   889.4599 logP:   1.9238
HBD:   7 HBA:   13
#Rotatable Bonds:   15 TPSA:   282.8
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Addition to a Triple Bond LYS 145 A 11.18 6.17 Cyanamide
Binding Affinity
-