- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.75 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 10T: 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid(Non-covalent)
10T.4: 12 residues within 4Å:- Chain A: R.99, E.179, E.180, S.183, Y.521, S.604, V.630, Y.636, Y.640, N.684, V.685, H.714
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:V.630, A:Y.636
- Hydrogen bonds: A:E.179, A:Y.521, A:S.604, A:Y.636
- Salt bridges: A:R.99, A:H.714
- pi-Stacking: A:Y.640
- pi-Cation interactions: A:R.99
10T.7: 13 residues within 4Å:- Chain B: R.99, E.179, E.180, S.183, Y.521, S.604, Y.605, V.630, Y.636, Y.640, N.684, V.685, H.714
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:V.630, B:Y.636
- Hydrogen bonds: B:E.180, B:Y.521, B:Y.521, B:S.604
- Salt bridges: B:R.99, B:H.714
- pi-Stacking: B:Y.640
- pi-Cation interactions: B:R.99
10T.14: 11 residues within 4Å:- Chain C: R.99, E.179, E.180, S.183, Y.521, S.604, V.630, Y.636, Y.640, V.685, H.714
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:V.630
- Hydrogen bonds: C:E.179, C:E.180, C:Y.521, C:S.604, C:Y.636
- Salt bridges: C:R.99, C:H.714
- pi-Stacking: C:Y.640
10T.17: 12 residues within 4Å:- Chain D: R.99, E.179, E.180, S.183, R.332, Y.521, S.604, V.630, Y.636, Y.640, N.684, H.714
11 PLIP interactions:11 interactions with chain D- Hydrophobic interactions: D:V.630, D:Y.636, D:Y.636
- Hydrogen bonds: D:E.179, D:E.180, D:Y.521, D:S.604
- Salt bridges: D:R.99, D:H.714
- pi-Stacking: D:Y.640
- pi-Cation interactions: D:R.99
- 10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.5: 1 residues within 4Å:- Chain A: N.124
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.124
NAG.6: 5 residues within 4Å:- Chain A: I.293, N.295, S.323, T.324, R.570
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.570
NAG.8: 2 residues within 4Å:- Chain B: N.59, S.61
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.61
- Water bridges: B:N.54
NAG.9: 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, B:N.124
NAG.10: 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.11: 2 residues within 4Å:- Chain B: W.161, N.255
No protein-ligand interaction detected (PLIP)NAG.15: 3 residues within 4Å:- Chain C: R.121, I.122, N.124
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.121
NAG.16: 2 residues within 4Å:- Chain C: W.161, N.255
No protein-ligand interaction detected (PLIP)NAG.18: 1 residues within 4Å:- Chain D: N.124
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:N.124
- Water bridges: D:R.121, D:R.121
NAG.19: 2 residues within 4Å:- Chain D: W.161, N.255
2 PLIP interactions:2 interactions with chain D- Water bridges: D:N.255, D:N.255
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Miyamoto, Y. et al., Discovery of a 3-Pyridylacetic Acid Derivative (TAK-100) as a Potent, Selective and Orally Active Dipeptidyl Peptidase IV (DPP-4) Inhibitor. J.Med.Chem. (2011)
- Release Date
- 2011-02-09
- Peptides
- Dipeptidyl peptidase 4: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.75 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 10T: 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid(Non-covalent)
- 10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Miyamoto, Y. et al., Discovery of a 3-Pyridylacetic Acid Derivative (TAK-100) as a Potent, Selective and Orally Active Dipeptidyl Peptidase IV (DPP-4) Inhibitor. J.Med.Chem. (2011)
- Release Date
- 2011-02-09
- Peptides
- Dipeptidyl peptidase 4: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D