SMTL ID : 3hac.1

The structure of DPP-4 in complex with piperidine fused imidazopyridine 34

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

9 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: 6 residues within 4Å: Chain A: E.29, V.40, N.42, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: R.109, I.110, 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.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558, E.639, D.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 Hydrogen bonds: B:E.294 NAG-NAG.8: 5 residues within 4Å: Chain B: 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 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.150, 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:N.112 Water bridges: B:N.112 NAG.15: 4 residues within 4Å: Chain B: I.281, N.283, S.311, R.558 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.558 Water bridges: 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:G.452

2 x 361: (7R,8R)-8-(2,4,5-trifluorophenyl)-6,7,8,9-tetrahydroimidazo[1,2-a:4,5-c']dipyridin-7-amine(Non-covalent)

361.12: 15 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673, H.702 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:Y.624 pi-Stacking: A:F.319, A:Y.624, A:Y.628 361.16: 14 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, Y.509, 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

Edmondson, S.D. et al., Aminopiperidine-fused imidazoles as dipeptidyl peptidase-IV inhibitors. Bioorg.Med.Chem.Lett. (2009)

Release Date

2009-07-21

Peptides

Dipeptidyl peptidase 4 soluble form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4 soluble form

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