SMTL ID : 3ccc.1 (1 other biounit)

Crystal Structure of Human DPP4 in complex with a benzimidazole derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 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: 4 residues within 4Å: Chain A: I.168, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: I.168, N.203, T.205, E.206 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.206

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

NAG.3: 4 residues within 4Å: Chain A: E.41, N.59, S.60, S.61 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: R.121, I.122, N.124 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.121 NAG.5: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.283 NAG.6: 3 residues within 4Å: Chain A: W.161, V.253, N.255 No protein-ligand interaction detected (PLIP) NAG.8: 6 residues within 4Å: Chain B: E.41, V.52, N.54, N.59, S.60, S.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.54, B:N.59 NAG.9: 2 residues within 4Å: Chain B: N.193, T.195 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain B: W.161, V.253, N.255 No protein-ligand interaction detected (PLIP)

2 x 7AC: 7-(aminomethyl)-6-(2-chlorophenyl)-1-methyl-1H-benzimidazole-5-carbonitrile(Non-covalent)

7AC.7: 13 residues within 4Å: Chain A: R.99, E.179, E.180, Y.521, W.603, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685, H.714 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.605, A:V.630, A:Y.636, A:V.685 Hydrogen bonds: A:R.99, A:E.180, A:Y.605, A:N.684 Water bridges: A:S.604 pi-Stacking: A:Y.640 pi-Cation interactions: A:R.99 Halogen bonds: A:N.684 7AC.11: 12 residues within 4Å: Chain B: R.99, E.179, E.180, Y.521, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685, H.714 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.605, B:V.630, B:Y.636, B:Y.636, B:V.685 Hydrogen bonds: B:E.179, B:S.604, B:Y.605, 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
A

B
B

Dipeptidyl peptidase 4

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