SMTL ID : 5t4b.1

Human DPP4 in complex with a ligand 34a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 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: 4 residues within 4Å: Chain A: R.109, I.110, P.111, N.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.109 NAG-NAG.2: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:N.234, A:E.294 Water bridges: A:E.271 NAG-NAG.3: 7 residues within 4Å: Chain A: I.281, N.283, M.310, 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 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.49 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 Hydrogen bonds: B:E.294 Water bridges: B:N.234, B:D.236 NAG-NAG.6: 5 residues within 4Å: Chain B: T.150, 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

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

NAG.8: 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:N.42 NAG.9: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194, A:E.194 Water bridges: A:T.227, A:K.229 NAG.10: 3 residues within 4Å: Chain A: W.149, V.241, N.243 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.243, A:N.243, A:N.243, A:N.243, A:N.243 NAG.13: 3 residues within 4Å: Chain B: R.109, I.110, N.112 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109 Water bridges: B:Y.80, B:N.112, B:N.112 NAG.14: 5 residues within 4Å: Chain B: I.281, N.283, S.311, T.312, R.558 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.283, B:R.558 Water bridges: B:N.283, B:N.283, B:N.283

2 x 75N: 2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-5-[(4-methylquinazolin-2-yl)methyl]-3H-imidazo[2,1-b]purin-4(5H)-one(Non-covalent)

75N.11: 12 residues within 4Å: Chain A: E.167, E.168, F.319, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673, H.702 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.591, A:W.591, A:Y.593, A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:E.167, A:E.167, A:Y.593, A:Y.624 Water bridges: A:R.87, A:W.591, A:S.592, A:S.592 pi-Stacking: A:Y.509, A:W.591 75N.15: 12 residues within 4Å: Chain B: E.167, E.168, F.319, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673, H.702 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.591, B:W.591, B:Y.593, B:V.618, B:Y.624, B:V.673 Hydrogen bonds: B:E.167, B:E.167, B:Y.593 Water bridges: B:R.87, B:Y.509, B:W.591, B:S.592, B:S.592, B:N.672 pi-Stacking: B:Y.509, B:W.591

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

NA.12: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pissarnitski, D.A. et al., Scaffold-hopping from xanthines to tricyclic guanines: A case study of dipeptidyl peptidase 4 (DPP4) inhibitors. Bioorg.Med.Chem. (2016)

Release Date

2016-10-05

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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