SMTL ID : 4g1f.6 (6 other biounits)

Crystal Structure of human Dipeptidyl Peptidase IV in complex with a pyridopyrimidinedione analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

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: 5 residues within 4Å: Chain A: I.168, Q.201, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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 0WG: 7-amino-6-(aminomethyl)-5-(2-bromophenyl)-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

0WG.2: 13 residues within 4Å: Chain A: R.99, E.179, E.180, Y.521, W.603, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685, H.714 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.605, A:V.630, A:Y.636, A:Y.636, A:Y.640, A:V.685 Hydrogen bonds: A:E.179, A:E.180, A:Y.605 Water bridges: A:E.179, A:E.180, A:E.180 pi-Stacking: A:Y.521, A:Y.640 Halogen bonds: A:R.99 0WG.6: 12 residues within 4Å: Chain B: R.99, E.179, E.180, Y.521, W.603, S.604, Y.605, V.630, Y.636, Y.640, V.685, H.714 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.605, B:V.630, B:Y.636, B:Y.636, B:Y.640, B:V.685 Hydrogen bonds: B:E.179, B:E.180, B:S.604, B:Y.605, B:Y.636 pi-Stacking: B:Y.640

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

NAG.3: 2 residues within 4Å: Chain A: I.122, N.124 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.124 NAG.4: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.193, A:T.195, A:T.195, A:E.283, A:E.283 NAG.7: 3 residues within 4Å: Chain B: R.121, I.122, N.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.121, B:N.124 Water bridges: B:N.124 NAG.8: 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

Lam, B. et al., Structure-based design of pyridopyrimidinediones as dipeptidyl peptidase IV inhibitors. Bioorg.Med.Chem.Lett. (2012)

Release Date

2013-02-27

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dipeptidyl peptidase 4

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