PDB Entry (2db4)
PDB ID: 2db4 Resolution: 2.4 Å Exp. Method: X-RAY DIFFRACTION
PMID: 21813759 DOI: 10.1073/pnas.1103287108
Protein
Protein Name: V-type sodium ATPase subunit K
Uniprot ID/ACC: P43457 (NTPK_ENTHA) Organism: Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)
Gene Symbol: ntpK Gene ID: 56786930
Protein Class: HYDROLASE
Ligand
Ligand Name:   N,N′-dicyclohexylcarbodiimide
Canonical SMILES:   C1CCCCC1N=C=NC2CCCCC2
Standard InChI:   InChI=1S/C13H22N2/c1-3-7-12(8-4-1)14-11-15-13-9-5-2-6-10-13/h12-13H,1-10H2
HET Code:   DCW PubChem:   10868
DrugBank:   - ChEMBL:   CHEMBL162598
Molecular Formula:   C13H22N2 Mol. Weight:   206.1783 logP:   3.8257
HBD:   0 HBA:   2
#Rotatable Bonds:   2 TPSA:   24.72
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Addition to a Double Bond GLU 139 I 26.78 6.8 Carbodiimide
Binding Affinity
-