SMTL ID : 3ccb.2 (1 other biounit)

Crystal Structure of Human DPP4 in complex with a benzimidazole derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: I.168, Q.201, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: I.168, Q.201, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: R.121, I.122, N.124 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.121 Hydrogen bonds: A:N.124 Water bridges: A:N.124 NAG.4: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.193 Hydrogen bonds: A:T.195, A:E.283 Water bridges: A:T.195 NAG.6: 3 residues within 4Å: Chain B: R.121, I.122, N.124 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.121 Hydrogen bonds: B:N.124 Water bridges: B:N.93 NAG.7: 2 residues within 4Å: Chain B: W.161, N.255 No protein-ligand interaction detected (PLIP)

2 x B2Y: 1-biphenyl-2-ylmethanamine(Non-covalent)

B2Y.5: 9 residues within 4Å: Chain A: R.99, E.179, E.180, Y.521, S.604, Y.636, Y.640, V.685, H.714 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.636, A:Y.636, A:V.685 Hydrogen bonds: A:E.179, A:E.180 pi-Stacking: A:Y.640 pi-Cation interactions: A:R.99 B2Y.8: 9 residues within 4Å: Chain B: R.99, E.179, E.180, Y.521, S.604, Y.636, Y.640, V.685, H.714 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.636, B:Y.636, B:V.685 Hydrogen bonds: B:E.180, B:Y.636 pi-Stacking: B:Y.640 pi-Cation interactions: B:R.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallace, M.B. et al., Structure-based design and synthesis of benzimidazole derivatives as dipeptidyl peptidase IV inhibitors. Bioorg.Med.Chem.Lett. (2008)

Release Date

2008-10-21

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dipeptidyl peptidase 4

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