› 3bjm

X-ray diffraction
2.35Å resolution

Crystal structure of human DPP-IV in complex with (1S,3S, 5S)-2-[(2S)-2-AMINO-2-(3-HYDROXYTRICYCLO[3.3.1.13,7]DEC-1- YL)ACETYL]-2-AZABICYCLO[3.1.0]HEXANE-3-CARBONITRILE (CAS), (1S,3S,5S)-2-((2S)-2-AMINO-2-(3-HYDROXYADAMANTAN-1- YL)ACETYL)-2-AZABICYCLO[3.1.0]HEXANE-3-CARBONITRILE (IUPAC), OR BMS-477118

Released:
DOI: 10.2210/pdb3bjm/pdb
PDB entry 3bjm coloured by chain, front view.
PDB entry 3bjm coloured by chain, side view.
PDB entry 3bjm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Involvement of DPP-IV catalytic residues in enzyme-saxagliptin complex formation.
Metzler WJ, Yanchunas J, Weigelt C, Kish K, Klei HE, Xie D, Zhang Y, Corbett M, Tamura JK, He B, Hamann LG, Kirby MS, Marcinkeviciene J
Protein Sci 17 240-50 (2008)
PMID: 18227430

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: 728 amino acids
Theoretical weight: 84.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P27487 (Residues: 39-766; Coverage: 95%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 65.278Å b: 67.954Å c: 423.816Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.213 0.253

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Citations

15 review citations

Nitrile-containing pharmaceuticals: efficacious roles of the nitrile pharmacophore.
Fleming et al. (2010)
14 more

10 mentions without citation

Nitriles: an attractive approach to the development of covalent inhibitors.
Bonatto et al. (2023)
9 more