SMTL ID : 3g0d.1 (5 other biounits)

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 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: 6 residues within 4Å: Chain A: I.168, Q.201, N.203, T.205, E.206, K.241 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: 6 residues within 4Å: Chain B: I.168, Q.201, N.203, T.205, E.206, K.241 No protein-ligand interaction detected (PLIP)

2 x XIH: 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE(Non-covalent)

XIH.4: 15 residues within 4Å: Chain A: R.99, E.179, E.180, F.331, Y.521, W.603, S.604, Y.605, G.606, V.630, Y.636, Y.640, N.684, V.685, H.714 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.605, A:V.630, A:Y.636, A:V.685 Hydrogen bonds: A:R.99, A:E.179, A:Y.605 Water bridges: A:R.99, A:Y.636 pi-Stacking: A:Y.521, A:Y.640 XIH.9: 14 residues within 4Å: Chain B: R.99, E.179, E.180, Y.521, W.603, S.604, Y.605, G.606, V.630, Y.636, Y.640, N.684, V.685, H.714 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.605, B:V.630, B:Y.636, B:Y.636, B:V.685 Hydrogen bonds: B:R.99, B:E.179, B:Y.605 pi-Stacking: B:Y.521, B:Y.640

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

NAG.5: 5 residues within 4Å: Chain A: V.52, N.54, N.59, S.60, S.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.54, A:N.59, A:S.61 NAG.6: 2 residues within 4Å: Chain A: I.122, N.124 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.124 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.570 Water bridges: A:N.295, A:N.295, A:N.295 NAG.10: 3 residues within 4Å: Chain B: Y.57, N.59, S.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.59, B:S.61 Water bridges: B:S.61 NAG.11: 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.12: 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.13: 2 residues within 4Å: Chain B: W.161, N.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255

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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