SMTL ID : 3vjk.1

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with MP-513

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 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: 7 residues within 4Å: Chain A: N.187, T.189, N.240, Q.276, E.277, Y.298, E.300 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.298 Hydrogen bonds: A:N.240, A:E.300, A:E.300, A:E.300 NAG-NAG.2: 4 residues within 4Å: Chain A: I.162, N.197, T.199, E.200 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 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.4: 7 residues within 4Å: Chain B: N.187, T.189, N.240, Q.276, E.277, Y.298, E.300 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.298 Hydrogen bonds: B:N.240, B:E.300 NAG-NAG.5: 4 residues within 4Å: Chain B: I.162, N.197, T.199, E.200 No protein-ligand interaction detected (PLIP)

2 x M51: {(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl}(1,3-thiazolidin-3-yl)methanone(Non-covalent)

M51.6: 15 residues within 4Å: Chain A: R.93, E.173, E.174, V.175, S.177, F.325, R.326, S.598, Y.599, V.624, W.627, Y.630, Y.634, N.678, V.679 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.325, A:R.326, A:Y.634 Hydrogen bonds: A:R.93, A:E.173, A:E.174, A:N.678 Water bridges: A:S.598 Salt bridges: A:E.174 pi-Stacking: A:F.325 M51.10: 14 residues within 4Å: Chain B: R.93, E.173, E.174, V.175, S.177, F.325, R.326, S.598, Y.599, V.624, Y.630, Y.634, N.678, V.679 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.325, B:R.326, B:Y.634 Hydrogen bonds: B:R.93, B:E.173, B:E.174, B:Y.630, B:N.678 Water bridges: B:S.598 Salt bridges: B:E.174 pi-Stacking: B:F.325

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

NAG.7: 5 residues within 4Å: Chain A: E.35, V.46, N.53, S.54, S.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53 NAG.8: 3 residues within 4Å: Chain A: E.41, N.43, N.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.41, A:N.43, A:N.60 NAG.9: 5 residues within 4Å: Chain A: N.289, M.316, S.317, T.318, R.564 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.289, A:R.564 NAG.11: 6 residues within 4Å: Chain B: E.35, V.46, N.48, N.53, S.54, S.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 NAG.12: 3 residues within 4Å: Chain B: R.115, I.116, N.118 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.115 Hydrogen bonds: B:R.115, B:N.118 Water bridges: B:R.115 NAG.13: 2 residues within 4Å: Chain B: W.155, N.249 No protein-ligand interaction detected (PLIP) NAG.14: 6 residues within 4Å: Chain B: I.287, N.289, Y.290, M.316, S.317, R.564 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.290 Hydrogen bonds: B:R.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, T. et al., Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes. Bioorg.Med.Chem. (2012)

Release Date

2012-10-24

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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