› 3g0d

X-ray diffraction
2.39Å resolution

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2

Released:
DOI: 10.2210/pdb3g0d/pdb
PDB entry 3g0d coloured by chain, front view.
PDB entry 3g0d coloured by chain, side view.
PDB entry 3g0d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design and synthesis of pyrimidinone and pyrimidinedione inhibitors of dipeptidyl peptidase IV.
Zhang Z, Wallace MB, Feng J, Stafford JA, Skene RJ, Shi L, Lee B, Aertgeerts K, Jennings A, Xu R, Kassel DB, Kaldor SW, Navre M, Webb DR, Gwaltney SL
J Med Chem 54 510-24 (2011)
PMID: 21186796

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
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151014 (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: Spodoptera frugiperda
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 XIH 4 x XIH
Ligand NAG 14 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P21
Unit cell:
a: 122.905Å b: 123.442Å c: 145.684Å
α: 90° β: 114.69° γ: 90°
R-values:
R R work R free
0.189 0.187 0.239
Expression system: Spodoptera frugiperda

Quick links

Citations

5 review citations

A survey of the role of nitrile groups in protein-ligand interactions.
Wang et al. (2018)
4 more

1 mention without citation

A Drug-Target Network-Based Approach to Evaluate the Efficacy of Medicinal Plants for Type II Diabetes Mellitus.
Gu et al. (2013)