SMTL ID : 5kby.3 (2 other biounits)

Crystal structure of dipeptidyl peptidase IV in complex with SYR-472

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-tetramer

Ligands

6 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: 3 residues within 4Å: Chain A: R.121, I.122, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: I.168, Q.201, N.203, T.205, E.206, K.241 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.205 Hydrogen bonds: A:E.206 NAG-NAG.3: 4 residues within 4Å: Chain A: W.161, V.253, N.255 Chain D: Q.115 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.161 Hydrogen bonds: D:Q.115 NAG-NAG.4: 5 residues within 4Å: Chain B: I.168, Q.201, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain C: I.168, N.203, T.205, E.206, K.241 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.205 NAG-NAG.16: 6 residues within 4Å: Chain D: I.168, Q.201, N.203, T.205, E.206, K.241 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.193, A:E.283, A:E.283 Water bridges: A:T.195 NAG.6: 6 residues within 4Å: Chain A: I.293, N.295, M.322, S.323, T.324, R.570 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.570 Water bridges: A:N.295 NAG.7: 4 residues within 4Å: Chain A: V.52, N.59, S.60, S.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.54, A:S.61 NAG.9: 4 residues within 4Å: Chain B: Y.57, N.59, S.60, S.61 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.59 Hydrogen bonds: B:S.61 Water bridges: B:Y.57 NAG.10: 1 residues within 4Å: Chain B: N.124 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain B: W.161, V.253, N.255 No protein-ligand interaction detected (PLIP) NAG.12: 6 residues within 4Å: Chain B: I.293, N.295, M.322, S.323, T.324, R.570 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.295, B:N.295, B:R.570 NAG.13: 4 residues within 4Å: Chain B: N.193, T.195, Q.282, E.283 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.193, B:E.283 Water bridges: B:T.195 NAG.17: 2 residues within 4Å: Chain C: I.122, N.124 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain C: W.161, V.253, N.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.255 NAG.19: 6 residues within 4Å: Chain C: I.293, N.295, M.322, S.323, T.324, R.570 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.295 Water bridges: C:S.323, C:T.324 NAG.21: 2 residues within 4Å: Chain D: R.121, N.124 No protein-ligand interaction detected (PLIP) NAG.22: 4 residues within 4Å: Chain D: N.193, T.195, Q.282, E.283 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.193, D:T.195, D:E.283 Water bridges: D:T.195 NAG.23: 3 residues within 4Å: Chain D: W.161, V.253, N.255 No protein-ligand interaction detected (PLIP) NAG.24: 6 residues within 4Å: Chain D: I.293, N.295, M.322, S.323, T.324, R.570 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.570 Water bridges: D:N.295

4 x 6RL: 2-[[6-[(3~{R})-3-azanylpiperidin-1-yl]-3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]methyl]-4-fluoranyl-benzenecarboni trile(Non-covalent)

6RL.8: 15 residues within 4Å: Chain A: R.99, E.179, E.180, F.331, Y.521, W.603, S.604, Y.605, V.630, W.633, Y.636, Y.640, N.684, V.685, H.714 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.331, A:Y.605, A:V.630, A:Y.636, A:Y.640, A:V.685 Hydrogen bonds: A:R.99, A:E.179, A:Y.521, A:Y.605 Water bridges: A:R.99, A:S.604, A:Y.636 pi-Stacking: A:Y.640 6RL.14: 15 residues within 4Å: Chain B: R.99, E.179, E.180, F.331, Y.521, W.603, S.604, Y.605, V.630, W.633, Y.636, Y.640, N.684, V.685, H.714 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.331, B:Y.605, B:V.630, B:Y.636, B:Y.636, B:Y.640, B:V.685 Hydrogen bonds: B:E.179, B:Y.605 Water bridges: B:R.99, B:S.604 pi-Stacking: B:Y.640 6RL.20: 15 residues within 4Å: Chain C: R.99, E.179, E.180, F.331, Y.521, W.603, S.604, Y.605, V.630, W.633, Y.636, Y.640, N.684, V.685, H.714 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.331, C:Y.605, C:V.630, C:Y.636, C:V.685 Hydrogen bonds: C:R.99, C:E.179, C:E.179, C:Y.605 Water bridges: C:S.604 pi-Stacking: C:Y.640 6RL.25: 15 residues within 4Å: Chain D: R.99, E.179, E.180, F.331, Y.521, W.603, S.604, Y.605, V.630, W.633, Y.636, Y.640, N.684, V.685, H.714 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.331, D:Y.605, D:V.630, D:Y.636, D:V.685 Hydrogen bonds: D:R.99, D:E.179, D:E.179, D:Y.605, D:Y.636 Water bridges: D:R.99, D:S.604 pi-Stacking: D:Y.640

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grimshaw, C.E. et al., Trelagliptin (SYR-472, Zafatek), Novel Once-Weekly Treatment for Type 2 Diabetes, Inhibits Dipeptidyl Peptidase-4 (DPP-4) via a Non-Covalent Mechanism. Plos One (2016)

Release Date

2016-07-13

Peptides

Dipeptidyl peptidase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dipeptidyl peptidase 4

Related Entries With Identical Sequence