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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-hexamer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: H.71, N.72, T.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.72 NAG.13: 4 residues within 4Å: Chain B: N.72, T.74, L.89, M.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.72 NAG.18: 3 residues within 4Å: Chain C: H.71, N.72, T.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.72 NAG.30: 4 residues within 4Å: Chain D: N.72, T.74, L.89, M.104 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.72 NAG.35: 3 residues within 4Å: Chain E: H.71, N.72, T.74 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.72 NAG.47: 4 residues within 4Å: Chain F: N.72, T.74, L.89, M.104 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.72

6 x 6VS: 2-~{tert}-butyl-4-(3-methoxypropylamino)-~{N}-(2-methylpropyl)-~{N}-[(3~{S},5~{R})-5-morpholin-4-ylcarbonylpiperidin-3-yl]pyrimidine-5-carboxamide(Non-covalent)

6VS.2: 22 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, L.118, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.33 Hydrogen bonds: A:Y.17, A:S.81, A:T.82, A:D.223, A:G.225 Water bridges: A:S.227, A:S.227 6VS.14: 23 residues within 4Å: Chain B: 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, L.221, D.223, T.224, G.225, A.226, I.302, T.306 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Q.16, B:P.115, B:F.116, B:L.118, B:L.118 Hydrogen bonds: B:Y.17, B:S.81, B:D.223, B:G.225 Water bridges: B:S.227, B:S.227 6VS.19: 22 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, L.118, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.33 Hydrogen bonds: C:Y.17, C:S.81, C:T.82, C:D.223, C:G.225 Water bridges: C:S.227, C:S.227 6VS.31: 23 residues within 4Å: Chain D: 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, L.221, D.223, T.224, G.225, A.226, I.302, T.306 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Q.16, D:P.115, D:F.116, D:L.118, D:L.118 Hydrogen bonds: D:Y.17, D:S.81, D:D.223, D:G.225 Water bridges: D:S.227, D:S.227 6VS.36: 22 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, L.118, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.33 Hydrogen bonds: E:Y.17, E:S.81, E:T.82, E:D.223, E:G.225, E:T.306 Water bridges: E:S.227, E:S.227 6VS.48: 23 residues within 4Å: Chain F: 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, L.221, D.223, T.224, G.225, A.226, I.302, T.306 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Q.16, F:P.115, F:F.116, F:L.118, F:L.118 Hydrogen bonds: F:Y.17, F:S.81, F:D.223, F:G.225 Water bridges: F:S.227, F:S.227

30 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 7 residues within 4Å: Chain A: D.14, A.279, D.280, V.282, F.283, A.296, R.318 Ligand excluded by PLIP DMS.4: 5 residues within 4Å: Chain A: L.51, Y.52 Chain E: Y.52 Ligands: DMS.21, DMS.38 Ligand excluded by PLIP DMS.5: 1 residues within 4Å: Chain A: K.47 Ligand excluded by PLIP DMS.6: 3 residues within 4Å: Chain A: H.188, K.272, E.273 Ligand excluded by PLIP DMS.7: 8 residues within 4Å: Chain A: K.247, R.248, L.249, F.250, D.251, Y.252, H.298, A.299 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: Y.57, H.58, M.117, A.119, E.120 Chain E: L.249 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: S.67, S.68, Y.69, K.70 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: E.75, S.86, G.87, F.88, T.109 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain B: E.273, Y.274, F.320 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: E.184, A.336 Chain B: S.6, V.7, I.8 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain C: D.14, A.279, D.280, V.282, F.283, A.296, R.318 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: Y.52 Chain C: L.51, Y.52 Ligands: DMS.4, DMS.38 Ligand excluded by PLIP DMS.22: 1 residues within 4Å: Chain C: K.47 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain C: H.188, K.272, E.273 Ligand excluded by PLIP DMS.24: 8 residues within 4Å: Chain C: K.247, R.248, L.249, F.250, D.251, Y.252, H.298, A.299 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: L.249 Chain C: Y.57, H.58, M.117, A.119, E.120 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain C: S.67, S.68, Y.69, K.70 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain C: E.75, S.86, G.87, F.88, T.109 Ligand excluded by PLIP DMS.33: 3 residues within 4Å: Chain D: E.273, Y.274, F.320 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain C: E.184, A.336 Chain D: S.6, V.7, I.8 Ligand excluded by PLIP DMS.37: 7 residues within 4Å: Chain E: D.14, A.279, D.280, V.282, F.283, A.296, R.318 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain C: Y.52 Chain E: L.51, Y.52 Ligands: DMS.4, DMS.21 Ligand excluded by PLIP DMS.39: 1 residues within 4Å: Chain E: K.47 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain E: H.188, K.272, E.273 Ligand excluded by PLIP DMS.41: 8 residues within 4Å: Chain E: K.247, R.248, L.249, F.250, D.251, Y.252, H.298, A.299 Ligand excluded by PLIP DMS.42: 6 residues within 4Å: Chain C: L.249 Chain E: Y.57, H.58, M.117, A.119, E.120 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain E: S.67, S.68, Y.69, K.70 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain E: E.75, S.86, G.87, F.88, T.109 Ligand excluded by PLIP DMS.50: 3 residues within 4Å: Chain F: E.273, Y.274, F.320 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain E: E.184, A.336 Chain F: S.6, V.7, I.8 Ligand excluded by PLIP

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

PEG.11: 2 residues within 4Å: Chain A: L.118, F.250 No protein-ligand interaction detected (PLIP) PEG.12: 4 residues within 4Å: Chain A: S.5, S.6, G.97, G.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.6 PEG.15: 5 residues within 4Å: Chain B: N.191, L.192, R.327, N.328, N.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.192 Water bridges: B:R.326, B:R.327 PEG.28: 2 residues within 4Å: Chain C: L.118, F.250 No protein-ligand interaction detected (PLIP) PEG.29: 4 residues within 4Å: Chain C: S.5, S.6, G.97, G.98 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.6 PEG.32: 5 residues within 4Å: Chain D: N.191, L.192, R.327, N.328, N.329 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.192 Water bridges: D:R.326, D:R.327 PEG.45: 2 residues within 4Å: Chain E: L.118, F.250 No protein-ligand interaction detected (PLIP) PEG.46: 4 residues within 4Å: Chain E: S.5, S.6, G.97, G.98 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.6 PEG.49: 5 residues within 4Å: Chain F: N.191, L.192, R.327, N.328, N.329 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.192 Water bridges: F:R.326, F:R.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imaeda, Y. et al., Discovery of TAK-272: A Novel, Potent, and Orally Active Renin Inhibitor. Acs Med.Chem.Lett. (2016)

Release Date

2016-11-16

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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