SMTL ID : 6b1e.1

The structure of DPP4 in complex with Vildagliptin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 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 No protein-ligand interaction detected (PLIP) 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 6 PLIP interactions: 6 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, A:E.294 NAG-NAG.3: 6 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558 No protein-ligand interaction detected (PLIP) 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: 7 residues within 4Å: Chain B: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 Water bridges: B:E.271, 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 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.150

2 x LF7: 2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-o ne(Covalent)

LF7.8: 12 residues within 4Å: Chain A: R.87, E.167, E.168, F.319, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.319, A:V.618, A:Y.624, A:Y.624, A:Y.628, A:V.673 Hydrogen bonds: A:R.87, A:E.167, A:E.167, A:Y.509, A:Y.593, A:Y.624, A:N.672 LF7.13: 13 residues within 4Å: Chain B: R.87, E.167, E.168, F.319, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.319, B:V.618, B:Y.624, B:Y.624, B:Y.628, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:E.167, B:Y.509, B:Y.509, B:Y.593, B:N.672 Water bridges: B:S.171, B:S.171

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

NAG.9: 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.10: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 8 PLIP interactions: 8 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, A:K.229 NAG.11: 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.14: 3 residues within 4Å: Chain B: R.109, I.110, N.112 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109 NAG.15: 5 residues within 4Å: Chain B: I.281, N.283, S.311, T.312, R.558 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.558 Water bridges: B:N.283, B:N.283, B:R.558

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

Berger, J.P. et al., A comparative study of the binding properties, dipeptidyl peptidase-4 (DPP-4) inhibitory activity and glucose-lowering efficacy of the DPP-4 inhibitors alogliptin, linagliptin, saxagliptin, sitagliptin and vildagliptin in mice. Endocrinol Diabetes Metab (2018)

Release Date

2017-09-27

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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