SMTL ID : 3o9v.2 (2 other biounits)

Crystal Structure of Human DPP4 Bound to TAK-986

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

3 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: I.168, N.203, T.205, E.206 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.205 NAG-NAG.2: 3 residues within 4Å: Chain A: W.161, V.253, N.255 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.161 NAG-NAG.3: 4 residues within 4Å: Chain B: I.168, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP)

2 x 10T: 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid(Non-covalent)

10T.4: 12 residues within 4Å: Chain A: R.99, E.179, E.180, S.183, Y.521, S.604, V.630, Y.636, Y.640, N.684, V.685, H.714 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.630, A:Y.636 Hydrogen bonds: A:E.179, A:Y.521, 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 10T.7: 13 residues within 4Å: Chain B: R.99, E.179, E.180, S.183, Y.521, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685, H.714 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.630, B:Y.636 Hydrogen bonds: B:E.180, B:Y.521, B:Y.521, B:S.604 Salt bridges: B:R.99, B:H.714 pi-Stacking: B:Y.640 pi-Cation interactions: B:R.99

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

NAG.5: 1 residues within 4Å: Chain A: N.124 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.124 NAG.6: 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.8: 2 residues within 4Å: Chain B: N.59, S.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.61 Water bridges: B:N.54 NAG.9: 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, B:N.124 NAG.10: 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.11: 2 residues within 4Å: Chain B: W.161, N.255 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

2011-02-09

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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