› 2jid

X-ray diffraction
2.8Å resolution

Human Dipeptidyl peptidase IV in complex with 1-(3,4-Dimethoxy-phenyl) -3-m-tolyl-piperidine-4-ylamine

Released:
DOI: 10.2210/pdb2jid/pdb
PDB entry 2jid coloured by chain, front view.
PDB entry 2jid coloured by chain, side view.
PDB entry 2jid coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
1,3-disubstituted 4-aminopiperidines as useful tools in the optimization of the 2-aminobenzo[a]quinolizine dipeptidyl peptidase IV inhibitors.
Lübbers T, Böhringer M, Gobbi L, Hennig M, Hunziker D, Kuhn B, Löffler B, Mattei P, Narquizian R, Peters JU, Ruff Y, Wessel HP, Wyss P
Bioorg Med Chem Lett 17 2966-70 (2007)
PMID: 17418568

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 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
Molecule details ›
Chains: A, B
Length: 736 amino acids
Theoretical weight: 85.21 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P27487 (Residues: 31-766; Coverage: 96%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand NAG 8 x NAG
Ligand GVB 2 x GVB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 65.251Å b: 66.821Å c: 423.948Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.223 0.303
Expression system: Komagataella pastoris

Quick links

Citations

4 review citations

Medicinal chemistry approaches to the inhibition of dipeptidyl peptidase-4 for the treatment of type 2 diabetes.
Havale et al. (2009)
3 more

3 mentions without citation

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites.
Cereto-Massagué et al. (2013)
2 more