SMTL ID : 2ajl.1

X-ray Structure of Novel Biaryl-Based Dipeptidyl peptidase IV inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

14 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 4 residues within 4Å: Chain A: N.42, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.42, A:N.47 NAG.2: 6 residues within 4Å: Chain A: I.156, Q.189, N.191, T.193, E.194 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.191, A:E.194, A:E.194 Water bridges: A:Q.189 NAG.3: 1 residues within 4Å: Ligands: NAG.2 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: W.149, N.243 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.243 Water bridges: A:N.243 NAG.5: 1 residues within 4Å: Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG.7: 6 residues within 4Å: Chain B: V.40, N.42, N.47, S.48, S.49 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.47 NAG.8: 1 residues within 4Å: Ligands: NAG.7 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain B: N.181, T.183, Q.270, E.271 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.181, B:E.271 NAG.10: 6 residues within 4Å: Chain B: N.234, D.236, E.271, Y.292, E.294 Ligands: NAG.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.234, B:N.234, B:Y.292, B:Y.292, B:E.294, B:E.294 NAG.11: 4 residues within 4Å: Chain B: I.156, N.191, T.193 Ligands: NAG.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191 NAG.12: 2 residues within 4Å: Chain B: E.194 Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: W.149, N.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.243, B:N.243 NAG.14: 5 residues within 4Å: Chain B: I.281, N.283, M.310, R.558 Ligands: NAG.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.283, B:N.283 NAG.15: 2 residues within 4Å: Chain B: D.640 Ligands: NAG.14 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.558

2 x JNH: 1-[2-(S)-AMINO-3-BIPHENYL-4-YL-PROPIONYL]-PYRROLIDINE-2-(S)-CARBONITRILE(Covalent)

JNH.6: 14 residues within 4Å: Chain A: R.87, E.167, E.168, V.169, S.171, F.319, R.320, Y.509, S.592, Y.593, Y.624, Y.628, N.672, H.702 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.319, A:F.319, A:F.319, A:Y.593, A:Y.624, A:Y.628 Hydrogen bonds: A:R.87, A:E.168, A:Y.509, A:Y.509, A:Y.593, A:N.672 JNH.16: 14 residues within 4Å: Chain B: R.87, E.167, E.168, V.169, S.171, F.319, R.320, Y.509, S.592, Y.593, Y.624, Y.628, N.672, H.702 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.319, B:F.319, B:F.319, B:R.320, B:Y.593, B:Y.624, B:Y.628 Hydrogen bonds: B:R.87, B:E.167, B:Y.509, B:Y.624, B:N.672, B:N.672

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, L. et al., Discovery, SAR, and X-ray structure of novel biaryl-based dipeptidyl peptidase IV inhibitors. Bioorg.Med.Chem.Lett. (2006)

Release Date

2005-11-08

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

Dipeptidyl peptidase 4

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