SMTL ID : 5koq.3 (2 other biounits)

Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: H.71, N.72, M.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.72 NAG.3: 2 residues within 4Å: Chain B: N.72, M.104 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain C: H.71, N.72, M.104 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.72 NAG.8: 2 residues within 4Å: Chain D: N.72, M.104 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain E: H.71, N.72, M.104 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.72 NAG.13: 2 residues within 4Å: Chain F: N.72, M.104 No protein-ligand interaction detected (PLIP)

6 x 6VR: 2-~{tert}-butyl-4-(furan-2-ylmethylamino)-~{N}-(2-methylpropyl)-~{N}-[(3~{S})-piperidin-3-yl]pyrimidine-5-carboxamide(Non-covalent)

6VR.2: 21 residues within 4Å: Chain A: T.15, Q.16, Y.17, V.33, D.35, G.37, Y.80, S.81, T.82, P.115, F.116, L.118, A.119, F.121, V.124, Y.159, D.223, T.224, G.225, A.226, S.227 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.16, A:Y.17, A:V.33, A:Y.80, A:F.116, A:A.119, A:V.124 Hydrogen bonds: A:D.35, A:G.225 6VR.4: 14 residues within 4Å: Chain B: T.15, Q.16, Y.17, V.33, D.35, G.37, P.115, L.118, V.124, D.223, T.224, G.225, A.226, S.227 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.17, B:V.33, B:V.33, B:L.118, B:V.124 Hydrogen bonds: B:D.35, B:G.225 Water bridges: B:S.227 6VR.7: 21 residues within 4Å: Chain C: T.15, Q.16, Y.17, V.33, D.35, G.37, Y.80, S.81, T.82, P.115, F.116, L.118, A.119, F.121, V.124, Y.159, D.223, T.224, G.225, A.226, S.227 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Q.16, C:Y.17, C:V.33, C:Y.80, C:F.116, C:A.119, C:V.124 Hydrogen bonds: C:D.35, C:T.82, C:G.225 6VR.9: 14 residues within 4Å: Chain D: T.15, Q.16, Y.17, V.33, D.35, G.37, P.115, L.118, V.124, D.223, T.224, G.225, A.226, S.227 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.17, D:V.33, D:V.33, D:L.118, D:V.124 Hydrogen bonds: D:D.35, D:G.225 Water bridges: D:S.227 6VR.12: 21 residues within 4Å: Chain E: T.15, Q.16, Y.17, V.33, D.35, G.37, Y.80, S.81, T.82, P.115, F.116, L.118, A.119, F.121, V.124, Y.159, D.223, T.224, G.225, A.226, S.227 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Q.16, E:Y.17, E:V.33, E:Y.80, E:F.116, E:A.119, E:V.124 Hydrogen bonds: E:D.35, E:G.225 6VR.14: 14 residues within 4Å: Chain F: T.15, Q.16, Y.17, V.33, D.35, G.37, P.115, L.118, V.124, D.223, T.224, G.225, A.226, S.227 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.17, F:V.33, F:V.33, F:L.118, F:V.124 Hydrogen bonds: F:D.35, F:G.225 Water bridges: F:S.227

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain B: L.192, R.327, N.328, N.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.192, B:R.327 Water bridges: B:N.329 PEG.10: 4 residues within 4Å: Chain D: L.192, R.327, N.328, N.329 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.192, D:R.327 Water bridges: D:N.329 PEG.15: 4 residues within 4Å: Chain F: L.192, R.327, N.328, N.329 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.192, F:R.327 Water bridges: F:N.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imaeda, Y. et al., Structure-based design of a new series of N-(piperidin-3-yl)pyrimidine-5-carboxamides as renin inhibitors. Bioorg.Med.Chem. (2016)

Release Date

2016-11-02

Peptides

Renin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Renin

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