SMTL ID : 2qoe.1

Human Dipeptidyl Peptidase IV in complex with a Triazolopiperazine-based beta amino acid Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NAG-NDG.1: 6 residues within 4Å: Chain A: E.29, V.40, N.42, N.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47 Water bridges: A:E.29, A:E.29 NAG-NDG.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194, A:E.194

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

NAG-NAG.2: 3 residues within 4Å: Chain A: I.110, P.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:N.234, A:E.294 NAG-NAG.5: 7 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558, D.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.558, A:R.558, A:D.640 NAG-NAG.6: 6 residues within 4Å: Chain B: E.29, V.40, N.42, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain B: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 NAG-NAG.8: 6 residues within 4Å: Chain B: T.150, I.156, Q.189, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: W.149, T.150, N.243 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.150

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

NAG.10: 3 residues within 4Å: Chain A: W.149, V.241, N.243 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: E.35, N.37, N.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37, B:N.37 NAG.14: 3 residues within 4Å: Chain B: R.109, I.110, N.112 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.109 NAG.15: 4 residues within 4Å: Chain B: I.281, N.283, S.311, R.558 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.558

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain A: G.452, L.453, R.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.453

2 x 448: (2R)-4-[(8R)-8-METHYL-2-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[1,5-A]PYRAZIN-7(8H)-YL]-4-OXO-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-AMINE(Non-covalent)

448.12: 15 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, Y.509, Y.547, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:Y.624 Water bridges: A:Y.509 pi-Stacking: A:F.319, A:Y.624, A:Y.628 448.16: 14 residues within 4Å: Chain B: R.87, E.167, E.168, F.319, Y.509, Y.547, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.673 Hydrogen bonds: B:E.167, B:E.168 pi-Stacking: B:F.319, B:Y.628

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kowalchick, J.E. et al., Design, synthesis, and biological evaluation of triazolopiperazine-based beta-amino amides as potent, orally active dipeptidyl peptidase IV (DPP-4) inhibitors. Bioorg.Med.Chem.Lett. (2007)

Release Date

2007-11-06

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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