SMTL ID : 3ccb.1 (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

3 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: 4 residues within 4Å: Chain A: I.168, N.203, T.205, E.206 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.205 NAG-NAG.2: 2 residues within 4Å: Chain A: W.161, N.255 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: I.168, N.203, T.205, E.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.206

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

NAG.4: 3 residues within 4Å: Chain A: V.52, N.59, S.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59, A:S.61 NAG.5: 2 residues within 4Å: Chain A: I.122, N.124 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.193, A:E.283, A:E.283 NAG.7: 6 residues within 4Å: Chain A: I.293, N.295, M.322, S.323, T.324, R.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.570 NAG.9: 2 residues within 4Å: Chain B: N.59, S.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61 NAG.10: 3 residues within 4Å: Chain B: R.121, I.122, N.124 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.121 Hydrogen bonds: B:N.124 NAG.11: 4 residues within 4Å: Chain B: N.193, T.195, Q.282, E.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.193, B:E.283 NAG.12: 2 residues within 4Å: Chain B: W.161, N.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255

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

B2Y.8: 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.180, A:Y.636 pi-Stacking: A:Y.640 pi-Cation interactions: A:R.99 B2Y.13: 10 residues within 4Å: Chain B: R.99, E.179, E.180, Y.521, S.604, V.630, Y.636, Y.640, V.685, H.714 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.630, B:Y.636, B:Y.636, B:V.685 Hydrogen bonds: B:E.180 pi-Stacking: B:Y.640

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
A

B
B

Dipeptidyl peptidase 4

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