SMTL ID : 5ism.1

Human DPP4 in complex with a novel 5,5,6-tricyclic pyrrolidine inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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.1: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:N.234, A:E.294, A:E.294 Water bridges: A:E.271, A:E.294 NAG-NAG.2: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: I.281, N.283, S.311, T.312, R.558, D.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.640 NAG-NAG.4: 5 residues within 4Å: Chain B: E.29, V.40, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain B: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 Water bridges: B:T.183, B:N.234, B:E.294 NAG-NAG.6: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 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.8: 5 residues within 4Å: Chain A: E.29, V.40, 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:N.42 NAG.9: 4 residues within 4Å: Chain A: R.109, I.110, P.111, N.112 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.109 Hydrogen bonds: A:R.109 NAG.10: 3 residues within 4Å: Chain A: W.149, V.241, N.243 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain B: I.281, N.283, S.311, T.312, R.558 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.283, 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 6DG: (2R,3S,5R)-2-(2,5-difluorophenyl)-5-(7H-pyrrolo[3',4':3,4]pyrazolo[1,5-a]pyrimidin-8(9H)-yl)oxan-3-amine(Non-covalent)

6DG.12: 14 residues within 4Å: Chain A: R.87, E.167, E.168, F.319, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673, H.702 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:E.167, A:E.167, A:Y.509, A:Y.624 Water bridges: A:R.87, A:S.171, A:Y.547 pi-Stacking: A:F.319, A:Y.628 6DG.14: 16 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, R.320, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673, H.702 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.618, B:Y.624, B:V.673 Hydrogen bonds: B:E.167, B:E.168, B:S.171, B:R.320, B:R.320 Water bridges: B:Y.509 pi-Stacking: B:F.319, B:Y.628 pi-Cation interactions: B:F.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cox, J.M. et al., The discovery of novel 5,6,5- and 5,5,6-tricyclic pyrrolidines as potent and selective DPP-4 inhibitors. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-05-11

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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