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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, T.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.72 NAG.15: 3 residues within 4Å: Chain B: N.72, T.74, M.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.72 Water bridges: B:G.135, B:R.136 NAG.25: 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.39: 3 residues within 4Å: Chain D: N.72, T.74, M.104 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.72 Water bridges: D:G.135, D:R.136 NAG.49: 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.63: 3 residues within 4Å: Chain F: N.72, T.74, M.104 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.72 Water bridges: F:G.135, F:R.136

6 x 6VU: 1-(4-methoxybutyl)-~{N}-(2-methylpropyl)-~{N}-[(3~{S},5~{R})-5-morpholin-4-ylcarbonylpiperidin-3-yl]benzimidazole-2-carboxamide(Non-covalent)

6VU.2: 25 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, A.119, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 Ligands: PEG.4, DMS.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.33, A:Y.80, A:P.115, A:P.115, A:A.119, A:F.121, A:F.121 Hydrogen bonds: A:Y.17, A:S.81, A:D.223 Water bridges: A:S.227 pi-Stacking: A:F.121 6VU.16: 27 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, L.118, A.119, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 Ligands: PEG.18, DMS.19, DMS.20, DMS.24 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.33, B:Y.80, B:P.115, B:L.118, B:A.119, B:F.121 Hydrogen bonds: B:Y.17, B:S.81, B:T.82, B:D.223, B:T.306 pi-Stacking: B:F.121 6VU.26: 25 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, A.119, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 Ligands: PEG.28, DMS.35 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.33, C:Y.80, C:P.115, C:P.115, C:A.119, C:F.121, C:F.121 Hydrogen bonds: C:Y.17, C:S.81, C:D.223 Water bridges: C:S.227 pi-Stacking: C:F.121 6VU.40: 27 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, L.118, A.119, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 Ligands: PEG.42, DMS.43, DMS.44, DMS.48 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.33, D:Y.80, D:P.115, D:L.118, D:A.119, D:F.121 Hydrogen bonds: D:Y.17, D:S.81, D:T.82, D:D.223, D:T.306 pi-Stacking: D:F.121 6VU.50: 25 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, A.119, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 Ligands: PEG.52, DMS.59 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.33, E:Y.80, E:P.115, E:P.115, E:A.119, E:F.121, E:F.121 Hydrogen bonds: E:Y.17, E:S.81, E:D.223 Water bridges: E:S.227 pi-Stacking: E:F.121 6VU.64: 27 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, L.118, A.119, F.121, V.124, Y.159, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 Ligands: PEG.66, DMS.67, DMS.68, DMS.72 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.33, F:Y.80, F:P.115, F:L.118, F:A.119, F:F.121 Hydrogen bonds: F:Y.17, F:S.81, F:D.223, F:T.306 pi-Stacking: F:F.121

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 7 residues within 4Å: Chain A: N.186, H.188, K.272, E.273, Y.274, F.333 Ligands: DMS.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.272 Water bridges: A:T.275 PGE.17: 7 residues within 4Å: Chain B: L.192, I.193, K.194, T.195, R.327, N.328, N.329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.193 Water bridges: B:T.195 PGE.27: 7 residues within 4Å: Chain C: N.186, H.188, K.272, E.273, Y.274, F.333 Ligands: DMS.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.272 Water bridges: C:T.275 PGE.41: 7 residues within 4Å: Chain D: L.192, I.193, K.194, T.195, R.327, N.328, N.329 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.193 Water bridges: D:T.195 PGE.51: 7 residues within 4Å: Chain E: N.186, H.188, K.272, E.273, Y.274, F.333 Ligands: DMS.62 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.272 Water bridges: E:T.275 PGE.65: 7 residues within 4Å: Chain F: L.192, I.193, K.194, T.195, R.327, N.328, N.329 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.193 Water bridges: F:T.195

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

PEG.4: 4 residues within 4Å: Chain A: T.82, S.227, H.298 Ligands: 6VU.2 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Water bridges: E:Y.57, E:Y.57, A:T.15 Hydrogen bonds: A:Y.228 PEG.5: 1 residues within 4Å: Chain A: K.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.194 PEG.6: 6 residues within 4Å: Chain A: S.206, G.208, S.209, T.211, S.266, E.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.206 PEG.18: 5 residues within 4Å: Chain B: T.82, P.115, L.118 Ligands: 6VU.16, DMS.20 2 PLIP interactions: 2 interactions with chain F Water bridges: F:E.258, F:E.258 PEG.28: 4 residues within 4Å: Chain C: T.82, S.227, H.298 Ligands: 6VU.26 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:Y.57, A:Y.57 Hydrogen bonds: C:Y.228 PEG.29: 1 residues within 4Å: Chain C: K.194 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.194 PEG.30: 6 residues within 4Å: Chain C: S.206, G.208, S.209, T.211, S.266, E.273 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.206 PEG.42: 5 residues within 4Å: Chain D: T.82, P.115, L.118 Ligands: 6VU.40, DMS.44 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.258 PEG.52: 4 residues within 4Å: Chain E: T.82, S.227, H.298 Ligands: 6VU.50 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Water bridges: C:Y.57, C:Y.57, E:T.15 Hydrogen bonds: E:Y.228 PEG.53: 1 residues within 4Å: Chain E: K.194 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.194 PEG.54: 6 residues within 4Å: Chain E: S.206, G.208, S.209, T.211, S.266, E.273 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.206 PEG.66: 5 residues within 4Å: Chain F: T.82, P.115, L.118 Ligands: 6VU.64, DMS.68 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.258, D:E.258

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

DMS.7: 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.8: 5 residues within 4Å: Chain A: S.81, M.300, D.301 Chain E: V.56, Y.57 Ligand excluded by PLIP DMS.9: 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.10: 6 residues within 4Å: Chain A: Y.57, H.58, M.117, A.119 Chain C: L.249, F.250 Ligand excluded by PLIP DMS.11: 8 residues within 4Å: Chain A: S.81, D.223, A.226, S.230, M.300, I.302, A.311 Ligands: 6VU.2 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: S.67, S.68, Y.69, K.70 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: L.76, L.78, G.87, F.88, G.106, V.108 Ligand excluded by PLIP DMS.14: 8 residues within 4Å: Chain A: G.185, N.186, L.335 Chain B: T.95, G.97, G.98, T.100 Ligands: PGE.3 Ligand excluded by PLIP DMS.19: 6 residues within 4Å: Chain B: S.81, D.223, A.226, M.300, A.311 Ligands: 6VU.16 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain B: T.15, Q.16, S.227, Y.228 Chain F: N.257 Ligands: 6VU.16, PEG.18 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain B: E.273, Y.274, F.320 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain B: L.76, L.78, G.87, F.88, G.106, V.108 Ligand excluded by PLIP DMS.23: 6 residues within 4Å: Chain A: E.184, L.335, A.336 Chain B: S.6, V.7, I.8 Ligand excluded by PLIP DMS.24: 6 residues within 4Å: Chain B: G.37, S.38, R.79, Y.80, I.134 Ligands: 6VU.16 Ligand excluded by PLIP DMS.31: 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.32: 5 residues within 4Å: Chain A: V.56, Y.57 Chain C: S.81, M.300, D.301 Ligand excluded by PLIP DMS.33: 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.34: 6 residues within 4Å: Chain C: Y.57, H.58, M.117, A.119 Chain E: L.249, F.250 Ligand excluded by PLIP DMS.35: 8 residues within 4Å: Chain C: S.81, D.223, A.226, S.230, M.300, I.302, A.311 Ligands: 6VU.26 Ligand excluded by PLIP DMS.36: 4 residues within 4Å: Chain C: S.67, S.68, Y.69, K.70 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain C: L.76, L.78, G.87, F.88, G.106, V.108 Ligand excluded by PLIP DMS.38: 8 residues within 4Å: Chain C: G.185, N.186, L.335 Chain D: T.95, G.97, G.98, T.100 Ligands: PGE.27 Ligand excluded by PLIP DMS.43: 6 residues within 4Å: Chain D: S.81, D.223, A.226, M.300, A.311 Ligands: 6VU.40 Ligand excluded by PLIP DMS.44: 7 residues within 4Å: Chain B: N.257 Chain D: T.15, Q.16, S.227, Y.228 Ligands: 6VU.40, PEG.42 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain D: E.273, Y.274, F.320 Ligand excluded by PLIP DMS.46: 6 residues within 4Å: Chain D: L.76, L.78, G.87, F.88, G.106, V.108 Ligand excluded by PLIP DMS.47: 6 residues within 4Å: Chain C: E.184, L.335, A.336 Chain D: S.6, V.7, I.8 Ligand excluded by PLIP DMS.48: 6 residues within 4Å: Chain D: G.37, S.38, R.79, Y.80, I.134 Ligands: 6VU.40 Ligand excluded by PLIP DMS.55: 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.56: 5 residues within 4Å: Chain C: V.56, Y.57 Chain E: S.81, M.300, D.301 Ligand excluded by PLIP DMS.57: 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.58: 6 residues within 4Å: Chain A: L.249, F.250 Chain E: Y.57, H.58, M.117, A.119 Ligand excluded by PLIP DMS.59: 8 residues within 4Å: Chain E: S.81, D.223, A.226, S.230, M.300, I.302, A.311 Ligands: 6VU.50 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain E: S.67, S.68, Y.69, K.70 Ligand excluded by PLIP DMS.61: 6 residues within 4Å: Chain E: L.76, L.78, G.87, F.88, G.106, V.108 Ligand excluded by PLIP DMS.62: 8 residues within 4Å: Chain E: G.185, N.186, L.335 Chain F: T.95, G.97, G.98, T.100 Ligands: PGE.51 Ligand excluded by PLIP DMS.67: 6 residues within 4Å: Chain F: S.81, D.223, A.226, M.300, A.311 Ligands: 6VU.64 Ligand excluded by PLIP DMS.68: 7 residues within 4Å: Chain D: N.257 Chain F: T.15, Q.16, S.227, Y.228 Ligands: 6VU.64, PEG.66 Ligand excluded by PLIP DMS.69: 3 residues within 4Å: Chain F: E.273, Y.274, F.320 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain F: L.76, L.78, G.87, F.88, G.106, V.108 Ligand excluded by PLIP DMS.71: 6 residues within 4Å: Chain E: E.184, L.335, A.336 Chain F: S.6, V.7, I.8 Ligand excluded by PLIP DMS.72: 6 residues within 4Å: Chain F: G.37, S.38, R.79, Y.80, I.134 Ligands: 6VU.64 Ligand excluded by PLIP

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. To be published

Release Date

2017-07-05

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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