› 3w2t

X-ray diffraction
2.36Å resolution

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with vildagliptin

Released:
DOI: 10.2210/pdb3w2t/pdb
PDB entry 3w2t coloured by chain, front view.
PDB entry 3w2t coloured by chain, side view.
PDB entry 3w2t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A comparative study of the binding modes of recently launched dipeptidyl peptidase IV inhibitors in the active site.
Nabeno M, Akahoshi F, Kishida H, Miyaguchi I, Tanaka Y, Ishii S, Kadowaki T
Biochem Biophys Res Commun 434 191-6 (2013)
PMID: 23501107

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151015 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Dipeptidyl peptidase 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 740 amino acids
Theoretical weight: 85.88 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P27487 (Residues: 33-766; Coverage: 96%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand LF7 2 x LF7
Ligand GOL 2 x GOL
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 118.216Å b: 126.237Å c: 137.089Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.18 0.231
Expression system: Spodoptera frugiperda

Quick links

Citations

38 review citations

DPP4 in Diabetes.
Röhrborn et al. (2015)
37 more

7 mentions without citation

Pyrrolidine in Drug Discovery: A Versatile Scaffold for Novel Biologically Active Compounds.
Li Petri et al. (2021)
6 more