SMTL ID : 3g0g.5 (5 other biounits)

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinone inhibitor 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

2 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)

1 x RUM: 2-({2-[(3R)-3-aminopiperidin-1-yl]-5-bromo-6-oxopyrimidin-1(6H)-yl}methyl)benzonitrile(Non-covalent)

RUM.3: 13 residues within 4Å: Chain A: R.99, E.179, E.180, F.331, Y.521, W.603, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685 11 PLIP interactions: 11 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:E.179, A:Y.605 pi-Stacking: A:Y.640

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

NAG.4: 3 residues within 4Å: Chain A: V.52, N.59, S.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.61 NAG.5: 2 residues within 4Å: Chain A: I.122, N.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.121, A:N.124 NAG.6: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.195, A:T.195 NAG.7: 3 residues within 4Å: Chain A: I.293, N.295, S.323 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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Dipeptidyl peptidase 4

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