PDB Entry (2gkj)
PDB ID: 2gkj Resolution: 1.7 Å Exp. Method: X-RAY DIFFRACTION
PMID: 16723397 DOI: 10.1073/pnas.0602537103
Protein
Protein Name: Diaminopimelate epimerase
Uniprot ID/ACC: P44859 (DAPF_HAEIN) Organism: Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Gene Symbol: dapF Gene ID: -
Protein Class: ISOMERASE
Ligand
Ligand Name:   DL-AZIDAP
Canonical SMILES:   N[C@@H](CCC[C@@]1(CN1)C(O)=O)C(O)=O
Standard InChI:   InChI=1S/C8H14N2O4/c9-5(6(11)12)2-1-3-8(4-10-8)7(13)14/h5,10H,1-4,9H2,(H,11,12)(H,13,14)/t5-,8+/m0/s1
HET Code:   ZDR PubChem:   11701228
DrugBank:   - ChEMBL:   -
Molecular Formula:   C8H14N2O4 Mol. Weight:   202.09535 logP:   -1.0048
HBD:   4 HBA:   4
#Rotatable Bonds:   6 TPSA:   122.56
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Aziridine Opening CYS 217 A 11.2 15.38 Aziridine
Binding Affinity
-