› 5kby

X-ray diffraction
2.24Å resolution

Crystal structure of dipeptidyl peptidase IV in complex with SYR-472

Released:
DOI: 10.2210/pdb5kby/pdb
PDB entry 5kby coloured by chain, front view.
PDB entry 5kby coloured by chain, side view.
PDB entry 5kby coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Trelagliptin (SYR-472, Zafatek), Novel Once-Weekly Treatment for Type 2 Diabetes, Inhibits Dipeptidyl Peptidase-4 (DPP-4) via a Non-Covalent Mechanism.
Grimshaw CE, Jennings A, Kamran R, Ueno H, Nishigaki N, Kosaka T, Tani A, Sano H, Kinugawa Y, Koumura E, Shi L, Takeuchi K
OpenAccess logo PLoS One 11 e0157509 (2016)
PMID: 27328054

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

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-151015 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Dipeptidyl peptidase 4 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 740 amino acids
Theoretical weight: 85.78 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P27487 (Residues: 39-766; Coverage: 95%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 15 x NAG
Ligand 6RL 4 x 6RL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P21
Unit cell:
a: 121.573Å b: 122.165Å c: 143.704Å
α: 90° β: 114.57° γ: 90°
R-values:
R R work R free
0.176 0.174 0.215
Expression system: unidentified baculovirus

Quick links

Citations

4 review citations

Once-weekly dipeptidyl peptidase-4 inhibitors for type 2 diabetes: a systematic review and meta-analysis.
Stoimenis et al. (2017)
3 more

2 mentions without citation

Discovery of Novel DPP-IV Inhibitors as Potential Candidates for the Treatment of Type 2 Diabetes mellitus Predicted by 3D QSAR Pharmacophore Models, Molecular Docking and de novo Evolution.
Musoev et al. (2019)
1 more