SMTL ID : 5lls.2 (1 other biounit)

Porcine dipeptidyl peptidase IV in complex with 8-(3-aminopiperidin-1-yl)-7-[(2-bromophenyl)methyl]-1,3-dimethyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

5 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: 9 residues within 4Å: Chain A: R.597, G.599, T.600, E.604, M.638, Y.682, N.685, S.686, R.691 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.597, A:R.597 NAG-NAG.2: 4 residues within 4Å: Chain B: E.73, N.75, N.92, D.96 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: T.188, I.194, Q.227, N.229, T.231, E.232, K.267 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: A.319, N.321, S.349, T.350, R.596, E.677, D.678 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.596, B:E.677 NAG-NAG.5: 9 residues within 4Å: Chain B: R.597, G.599, T.600, E.604, M.638, Y.682, N.685, S.686, R.691 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.597, B:R.597, B:E.604

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

NAG.6: 4 residues within 4Å: Chain A: L.78, N.85, S.86, S.87 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: E.73, N.75, N.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.74, A:N.75, A:N.92 NAG.8: 7 residues within 4Å: Chain A: T.188, I.194, Q.227, N.229, T.231, E.232, K.267 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.188, A:I.194 Hydrogen bonds: A:N.229, A:T.231, A:E.232, A:K.267 Water bridges: A:E.232 NAG.9: 1 residues within 4Å: Chain A: N.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.279 NAG.10: 2 residues within 4Å: Chain A: N.321, S.349 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.321 NAG.14: 3 residues within 4Å: Chain B: N.85, S.86, S.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.85, B:S.87 NAG.15: 2 residues within 4Å: Chain B: P.278, N.279 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.279, B:N.279

4 x 6Z8: 8-[(3~{R})-3-azanylpiperidin-1-yl]-7-[(2-bromophenyl)methyl]-1,3-dimethyl-purine-2,6-dione(Non-covalent)

6Z8.11: 13 residues within 4Å: Chain A: R.125, E.205, E.206, F.357, Y.547, W.629, S.630, Y.631, Y.662, Y.666, N.710, V.711, H.740 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.662, A:V.711 Hydrogen bonds: A:E.205, A:E.206, A:Y.631, A:Y.662 pi-Stacking: A:Y.547 6Z8.13: 5 residues within 4Å: Chain A: W.187, P.278, A.280, S.281, V.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.282 pi-Stacking: A:W.187, A:W.187 Halogen bonds: A:P.278 6Z8.16: 13 residues within 4Å: Chain B: R.125, E.205, E.206, F.357, Y.547, W.629, S.630, Y.631, Y.662, Y.666, N.710, V.711, H.740 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.662, B:V.711 Hydrogen bonds: B:E.205, B:E.206, B:Y.631, B:Y.662 pi-Stacking: B:Y.547 6Z8.18: 5 residues within 4Å: Chain B: W.187, P.278, A.280, S.281, V.282 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.282 pi-Stacking: B:W.187, B:W.187, B:W.187 Halogen bonds: B:P.278

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 6 residues within 4Å: Chain A: A.360, E.361, H.363, I.374, G.406, I.407 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.361, A:I.407 Water bridges: A:E.361 Salt bridges: A:H.363 SO4.17: 6 residues within 4Å: Chain B: E.361, H.363, I.374, I.405, G.406, I.407 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.361, B:I.407, B:I.407 Salt bridges: B:H.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schnapp, G. et al., Comparative Analysis of Binding Kinetics and Thermodynamics of Dipeptidyl Peptidase-4 Inhibitors and Their Relationship to Structure. J.Med.Chem. (2016)

Release Date

2016-09-14

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dipeptidyl peptidase 4

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