SMTL ID : 3vjm.1

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with a prolylthiazolidine inhibitor #1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

5 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: 8 residues within 4Å: Chain A: N.187, T.189, F.190, N.240, Q.276, E.277, Y.298, E.300 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.190, A:Y.298 Hydrogen bonds: A:N.240, A:E.300, A:E.300 Water bridges: A:T.189 NAG-NAG.2: 3 residues within 4Å: Chain A: W.155, T.156, N.249 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.156 NAG-NAG.3: 8 residues within 4Å: Chain B: N.187, T.189, F.190, N.240, Q.276, E.277, Y.298, E.300 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.190, B:Y.298 Hydrogen bonds: B:N.240, B:E.300 NAG-NAG.4: 5 residues within 4Å: Chain B: I.162, N.197, T.199, E.200, K.235 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain B: I.287, N.289, M.316, S.317, T.318, R.564, E.645, D.646 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.646

2 x W61: 1,3-thiazolidin-3-yl[(2S,4S)-4-{4-[2-(trifluoromethyl)quinolin-4-yl]piperazin-1-yl}pyrrolidin-2-yl]methanone(Non-covalent)

W61.6: 14 residues within 4Å: Chain A: R.93, E.173, E.174, F.325, R.326, Y.553, S.598, Y.599, V.624, W.627, Y.630, Y.634, N.678, V.679 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.325, A:F.325, A:F.325, A:Y.634 Hydrogen bonds: A:R.93, A:E.173, A:E.174, A:N.678 Water bridges: A:Y.553, A:S.598 Salt bridges: A:E.174 W61.11: 14 residues within 4Å: Chain B: R.93, E.173, E.174, F.325, R.326, Y.553, S.598, Y.599, V.624, W.627, Y.630, Y.634, N.678, V.679 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.325, B:F.325, B:F.325, B:Y.634 Hydrogen bonds: B:R.93, B:E.173, B:E.174, B:Y.630, B:N.678 Water bridges: B:Y.553, B:S.598 Salt bridges: B:E.174

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

NAG.7: 4 residues within 4Å: Chain A: V.46, N.53, S.54, S.55 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.46 Hydrogen bonds: A:N.53 NAG.8: 3 residues within 4Å: Chain A: E.41, N.43, N.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.41, A:N.43 NAG.9: 6 residues within 4Å: Chain A: I.162, Q.195, N.197, T.199, E.200, K.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.199, A:E.200 Water bridges: A:Q.195, A:N.197 NAG.10: 6 residues within 4Å: Chain A: I.287, N.289, M.316, S.317, T.318, R.564 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.289, A:R.564 Water bridges: A:N.289 NAG.12: 6 residues within 4Å: Chain B: E.35, V.46, N.48, N.53, S.54, S.55 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.46 Water bridges: B:E.35, B:N.48 NAG.13: 4 residues within 4Å: Chain B: R.115, I.116, P.117, N.118 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.115 Hydrogen bonds: B:R.115, B:R.115 NAG.14: 3 residues within 4Å: Chain B: W.155, V.247, N.249 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, T. et al., Fused bicyclic heteroarylpiperazine-substituted l-prolylthiazolidines as highly potent DPP-4 inhibitors lacking the electrophilic nitrile group. Bioorg.Med.Chem. (2012)

Release Date

2012-08-15

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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