- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 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
13 PLIP interactions:13 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:E.180, B:S.604, B:Y.605, B:Y.636
- pi-Stacking: B:Y.640
0WG.12: 13 residues within 4Å:- Chain C: 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
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:Y.521, C:Y.605, C:Y.605, C:V.630, C:Y.636, C:Y.640, C:V.685
- Hydrogen bonds: C:E.180, C:Y.605, C:Y.636
- Water bridges: C:E.180
- pi-Stacking: C:Y.640
0WG.17: 12 residues within 4Å:- Chain D: R.99, E.179, E.180, Y.521, W.603, S.604, Y.605, V.630, Y.636, Y.640, V.685, H.714
13 PLIP interactions:13 interactions with chain D- Hydrophobic interactions: D:Y.605, D:Y.605, D:V.630, D:Y.636, D:Y.636, D:Y.640, D:V.685
- Hydrogen bonds: D:E.180, D:Y.605
- Water bridges: D:E.180, D:E.180
- pi-Stacking: D:Y.521, D:Y.640
- 12 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)NAG.13: 4 residues within 4Å:- Chain C: V.52, N.59, S.60, S.61
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:V.52
- Hydrogen bonds: C:N.59, C:S.61
NAG.14: 2 residues within 4Å:- Chain C: R.121, N.124
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.124
- Water bridges: C:N.124
NAG.15: 4 residues within 4Å:- Chain C: N.193, T.195, Q.282, E.283
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:N.193, C:E.283, C:E.283
NAG.16: 5 residues within 4Å:- Chain C: I.293, N.295, S.323, T.324, R.570
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.570
NAG.18: 2 residues within 4Å:- Chain D: N.59, S.61
No protein-ligand interaction detected (PLIP)NAG.19: 3 residues within 4Å:- Chain D: I.122, P.123, N.124
1 PLIP interactions:1 interactions with chain D- Water bridges: D:N.124
NAG.20: 4 residues within 4Å:- Chain D: N.193, T.195, Q.282, E.283
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:N.193, D:E.283
NAG.21: 2 residues within 4Å:- Chain D: W.161, N.255
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:N.255
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
DC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x 0WG: 7-amino-6-(aminomethyl)-5-(2-bromophenyl)-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione(Non-covalent)
- 12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
DC
AD
B