› 5y7k

X-ray diffraction
2.51Å resolution

Crystal structure of human DPP4 in complex with inhibitor1

Released:
DOI: 10.2210/pdb5y7k/pdb
PDB entry 5y7k coloured by chain, front view.
PDB entry 5y7k coloured by chain, side view.
PDB entry 5y7k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Unique binding mode of Evogliptin with human dipeptidyl peptidase IV.
Lee HK, Kim MK, Kim HD, Kim HJ, Kim JW, Lee JO, Kim CW, Kim EE
Biochem Biophys Res Commun 494 452-459 (2017)
PMID: 29061303

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
Macromolecule:
Dipeptidyl peptidase 4 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 728 amino acids
Theoretical weight: 84.46 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P27487 (Residues: 39-766; Coverage: 95%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 8VU 4 x 8VU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P21
Unit cell:
a: 119.365Å b: 131.92Å c: 123.409Å
α: 90° β: 89.99° γ: 90°
R-values:
R R work R free
0.207 0.205 0.241
Expression system: Trichoplusia ni

Quick links

Citations

1 review citation

The perceptions of natural compounds against dipeptidyl peptidase 4 in diabetes: from in silico to in vivo.
Lin et al. (2019)
2 other articles

3 mentions without citation

Improvements in HOMA indices and pancreatic endocrinal tissues in type 2-diabetic rats by DPP-4 inhibition and antioxidant potential of an ethanol fruit extract of Withania coagulans.
Ram et al. (2021)
2 more