PDB Entry (3w2t)
PDB ID: 3w2t Resolution: 2.36 Å Exp. Method: X-RAY DIFFRACTION
PMID: 23501107 DOI: 10.1016/j.bbrc.2013.03.010
Protein
Protein Name: Dipeptidyl peptidase 4
Uniprot ID/ACC: P27487 (DPP4_HUMAN) Organism: Homo sapiens (Human)
Gene Symbol: DPP4 Gene ID: 1803
Protein Class: HYDROLASE
Ligand
Ligand Name:   vildagliptin
Canonical SMILES:   OC12CC3CC(C1)CC(C3)(C2)NCC(=O)N1CCC[C@H]1C#N
Standard InChI:   InChI=1S/C17H25N3O2/c18-9-14-2-1-3-20(14)15(21)10-19-16-5-12-4-13(6-16)8-17(22,7-12)11-16/h12-14,19,22H,1-8,10-11H2/t12?,13?,14-,16?,17?/m0/s1
HET Code:   LF7 PubChem:   6918537
DrugBank:   DB04876 ChEMBL:   CHEMBL142703
Molecular Formula:   C17H25N3O2 Mol. Weight:   303.19467 logP:   1.17428
HBD:   2 HBA:   4
#Rotatable Bonds:   3 TPSA:   76.36
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Addition to a Triple Bond SER 630 A 19.59 - Nitrile
Binding Affinity
Database Name Value
PDBBind IC50 : 29.2 nM
BindingDB IC50 : 80.1 nM , IC50 : 3.5 nM