SMTL ID : 3g0c.1 (5 other biounits)

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 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 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: W.161, N.255 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: I.168, N.203, T.205 No protein-ligand interaction detected (PLIP)

2 x RUF: 7-(2-chlorobenzyl)-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-1H-purine-2,6-dione(Non-covalent)

RUF.4: 11 residues within 4Å: Chain A: E.179, E.180, Y.521, W.603, S.604, Y.605, Y.636, Y.640, N.684, V.685, H.714 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.636, A:V.685 Hydrogen bonds: A:E.180, A:S.604, A:Y.605 pi-Stacking: A:Y.521 RUF.9: 12 residues within 4Å: Chain B: E.179, E.180, Y.521, W.603, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685, H.714 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.636, B:V.685 Hydrogen bonds: B:E.180, B:S.604, B:Y.605 Water bridges: B:R.99 pi-Stacking: B:Y.521

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

NAG.5: 5 residues within 4Å: Chain A: E.41, V.52, N.59, S.60, S.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59 NAG.6: 2 residues within 4Å: Chain A: R.121, N.124 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.121 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:T.195, A:E.283, A:E.283 NAG.8: 6 residues within 4Å: Chain A: I.293, N.295, M.322, S.323, T.324, R.570 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.570 Water bridges: A:N.295, A:N.295 NAG.10: 1 residues within 4Å: Chain B: N.59 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.59, B:N.59 NAG.11: 4 residues within 4Å: Chain B: R.121, I.122, P.123, N.124 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.121 Hydrogen bonds: B:R.121 Water bridges: B:N.124 NAG.12: 4 residues within 4Å: Chain B: N.193, T.195, Q.282, E.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.283 Water bridges: B:T.195 NAG.13: 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

Zhang, Z. et al., Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV. J.Med.Chem. (2011)

Release Date

2010-02-16

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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