SMTL ID : 3o95.1 (2 other biounits)

Crystal Structure of Human DPP4 Bound to TAK-100

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

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: 2 residues within 4Å: Chain A: R.121, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.59, S.60, S.61 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: I.168, N.203, T.205, E.206 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.205 NAG-NAG.4: 4 residues within 4Å: Chain A: W.161, V.253, N.255 Chain D: Q.115 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: Y.57, N.59, S.61 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: I.168, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain D: I.168, Q.201, N.203, T.205, E.206, K.241 No protein-ligand interaction detected (PLIP)

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

NAG.7: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.193, A:E.283, A:E.283 NAG.8: 5 residues within 4Å: Chain A: I.293, N.295, S.323, T.324, R.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.570 NAG.10: 3 residues within 4Å: Chain B: R.121, I.122, N.124 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.121 Hydrogen bonds: B:N.124 Water bridges: B:N.124 NAG.11: 2 residues within 4Å: Chain B: W.161, N.255 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.255 NAG.12: 4 residues within 4Å: Chain B: I.293, N.295, M.322, S.323 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.295 NAG.16: 3 residues within 4Å: Chain C: R.121, I.122, N.124 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.124 Water bridges: C:R.121 NAG.17: 2 residues within 4Å: Chain C: W.161, N.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.255 NAG.18: 3 residues within 4Å: Chain B: S.307 Chain C: I.293, N.295 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.295, C:R.570 NAG.20: 1 residues within 4Å: Chain D: N.124 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.124, D:N.124 NAG.21: 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.22: 2 residues within 4Å: Chain D: W.161, N.255 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.255, D:N.255 NAG.23: 4 residues within 4Å: Chain D: L.493, N.494, F.498, R.555 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.579, D:D.579

4 x 01T: [5-(aminomethyl)-6-(2,2-dimethylpropyl)-2-ethyl-4-(4-methylphenyl)pyridin-3-yl]acetic acid(Non-covalent)

01T.9: 12 residues within 4Å: Chain A: R.99, E.179, E.180, S.183, F.331, Y.521, S.604, V.630, Y.636, Y.640, V.685, H.714 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.331, A:V.630, A:Y.636 Hydrogen bonds: A:E.179, A:S.604, A:S.604, A:Y.636 Salt bridges: A:R.99, A:H.714 pi-Stacking: A:Y.640 pi-Cation interactions: A:R.99 01T.13: 13 residues within 4Å: Chain B: R.99, E.179, E.180, S.183, F.331, Y.521, S.604, Y.605, V.630, Y.636, Y.640, N.684, H.714 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.331, B:V.630, B:Y.636 Hydrogen bonds: B:E.179, B:S.604, B:S.604 Salt bridges: B:R.99, B:H.714 pi-Stacking: B:Y.640 pi-Cation interactions: B:R.99 01T.19: 13 residues within 4Å: Chain C: R.99, E.179, E.180, S.183, F.331, Y.521, S.604, Y.605, V.630, Y.636, Y.640, V.685, H.714 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.331, C:V.630, C:Y.636, C:V.685 Hydrogen bonds: C:E.179, C:E.180, C:S.604, C:Y.636 Salt bridges: C:R.99, C:H.714 pi-Stacking: C:Y.640 pi-Cation interactions: C:R.99 01T.24: 12 residues within 4Å: Chain D: R.99, E.179, E.180, S.183, F.331, Y.521, S.604, Y.605, V.630, Y.636, Y.640, H.714 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.331, D:V.630, D:Y.636 Hydrogen bonds: D:E.179, D:E.180, D:S.604 Salt bridges: D:R.99, D:H.714 pi-Stacking: D:Y.640 pi-Cation interactions: D:R.99

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.14: 6 residues within 4Å: Chain B: I.269 Chain C: I.168, N.203, T.205, E.206, K.241 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyamoto, Y. et al., Discovery of a 3-Pyridylacetic Acid Derivative (TAK-100) as a Potent, Selective and Orally Active Dipeptidyl Peptidase IV (DPP-4) Inhibitor. J.Med.Chem. (2011)

Release Date

2011-01-26

Peptides

Dipeptidyl peptidase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dipeptidyl peptidase 4

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