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

Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

3 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.8: 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.15: 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

6 x 7EJ: 1-(4-methoxybutyl)-N-(2-methylpropyl)-N-[(3S,5R)-5-(morpholine-4-carbonyl)piperidin-3-yl]-5-phenyl-1H-pyrrole-2-carboxamide(Non-covalent)

7EJ.2: 24 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, 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:Q.16, A:P.115, A:F.116, A:A.119, A:V.124 Hydrogen bonds: A:Y.17, A:S.81, A:D.223 7EJ.6: 22 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, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.115, B:L.118, B:F.121, B:F.121, B:V.124 Hydrogen bonds: B:Y.17, B:S.81, B:D.223, B:T.306 7EJ.9: 24 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, 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:Q.16, C:P.115, C:F.116, C:A.119, C:V.124 Hydrogen bonds: C:Y.17, C:S.81, C:D.223 7EJ.13: 22 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, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.115, D:L.118, D:F.121, D:F.121, D:V.124 Hydrogen bonds: D:Y.17, D:S.81, D:D.223 7EJ.16: 24 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, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Q.16, E:P.115, E:F.116, E:A.119, E:V.124 Hydrogen bonds: E:Y.17, E:S.81, E:D.223 7EJ.20: 22 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, L.221, D.223, T.224, G.225, A.226, S.227, I.302, T.306 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:P.115, F:L.118, F:F.121, F:F.121, F:V.124 Hydrogen bonds: F:Y.17, F:S.81, F:D.223

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

DMS.3: 6 residues within 4Å: Chain A: S.81, T.82, M.300, D.301 Chain C: V.56, Y.57 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A pi-Cation interactions: C:Y.57 Hydrogen bonds: A:D.301 DMS.4: 7 residues within 4Å: Chain A: D.14, A.279, D.280, V.282, F.283, A.296, R.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.318 pi-Cation interactions: A:F.283 DMS.5: 8 residues within 4Å: Chain A: K.247, R.248, L.249, F.250, D.251, Y.252, H.298, A.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.299 DMS.10: 6 residues within 4Å: Chain C: S.81, T.82, M.300, D.301 Chain E: V.56, Y.57 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C pi-Cation interactions: E:Y.57 Hydrogen bonds: C:D.301 DMS.11: 7 residues within 4Å: Chain C: D.14, A.279, D.280, V.282, F.283, A.296, R.318 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.318 pi-Cation interactions: C:F.283 DMS.12: 8 residues within 4Å: Chain C: K.247, R.248, L.249, F.250, D.251, Y.252, H.298, A.299 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.299 DMS.17: 6 residues within 4Å: Chain A: V.56, Y.57 Chain E: S.81, T.82, M.300, D.301 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.301 pi-Cation interactions: A:Y.57 DMS.18: 7 residues within 4Å: Chain E: D.14, A.279, D.280, V.282, F.283, A.296, R.318 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.318 pi-Cation interactions: E:F.283 DMS.19: 8 residues within 4Å: Chain E: K.247, R.248, L.249, F.250, D.251, Y.252, H.298, A.299 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.299

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

PEG.7: 4 residues within 4Å: Chain B: L.192, R.327, N.328, N.329 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.192 PEG.14: 4 residues within 4Å: Chain D: L.192, R.327, N.328, N.329 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.192 PEG.21: 4 residues within 4Å: Chain F: L.192, R.327, N.328, N.329 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tokuhara, H. et al., Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor. To be published

Release Date

2017-10-18

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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