SMTL ID : 5sz9.3 (2 other biounits)

Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 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.73, N.74, T.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.74 NAG.6: 2 residues within 4Å: Chain B: N.74, M.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.76, B:T.76 Water bridges: B:N.74 NAG.10: 3 residues within 4Å: Chain C: H.73, N.74, T.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.74 NAG.15: 2 residues within 4Å: Chain D: N.74, M.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.76 Water bridges: D:N.74 NAG.19: 3 residues within 4Å: Chain E: H.73, N.74, T.76 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.74 NAG.24: 2 residues within 4Å: Chain F: N.74, M.106 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.76, F:T.76 Water bridges: F:N.74

6 x 74Y: (azepan-1-yl)(2-{[(furan-2-yl)methyl]amino}-6-methylpyridin-3-yl)methanone(Non-covalent)

74Y.2: 16 residues within 4Å: Chain A: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, L.120, A.121, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.19, A:V.35, A:Y.82, A:Y.82, A:Y.82, A:F.123, A:V.126 Water bridges: A:S.229, A:S.229 pi-Stacking: A:F.123 74Y.7: 16 residues within 4Å: Chain B: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, F.118, L.120, A.121, F.123, V.126, T.226, G.227, A.228, S.229 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.35, B:V.35, B:Y.82, B:Y.82, B:Y.82, B:T.84, B:F.118, B:F.118, B:L.120, B:F.123, B:V.126 Hydrogen bonds: B:T.84, B:G.227 Water bridges: B:S.229 pi-Stacking: B:F.123 74Y.11: 16 residues within 4Å: Chain C: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, L.120, A.121, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.19, C:V.35, C:Y.82, C:Y.82, C:Y.82, C:F.123, C:V.126 Water bridges: C:S.229, C:S.229 pi-Stacking: C:F.123 74Y.16: 16 residues within 4Å: Chain D: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, F.118, L.120, A.121, F.123, V.126, T.226, G.227, A.228, S.229 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.35, D:V.35, D:Y.82, D:Y.82, D:Y.82, D:T.84, D:F.118, D:F.118, D:L.120, D:F.123, D:V.126 Hydrogen bonds: D:T.84, D:G.227 Water bridges: D:S.229 pi-Stacking: D:F.123 74Y.20: 16 residues within 4Å: Chain E: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, L.120, A.121, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.19, E:V.35, E:Y.82, E:Y.82, E:Y.82, E:F.123, E:V.126 Water bridges: E:S.229, E:S.229 pi-Stacking: E:F.123 74Y.25: 16 residues within 4Å: Chain F: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, F.118, L.120, A.121, F.123, V.126, T.226, G.227, A.228, S.229 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:V.35, F:V.35, F:Y.82, F:Y.82, F:Y.82, F:T.84, F:F.118, F:F.118, F:L.120, F:F.123, F:V.126 Hydrogen bonds: F:T.84, F:G.227 Water bridges: F:S.229 pi-Stacking: F:F.123

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

PEG.3: 4 residues within 4Å: Chain A: L.53, Y.54 Chain C: Y.54, E.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.51, A:L.53 Water bridges: A:Y.54 PEG.4: 7 residues within 4Å: Chain A: N.188, F.189, H.190, K.274, Y.276, F.322, F.335 No protein-ligand interaction detected (PLIP) PEG.5: 3 residues within 4Å: Chain A: T.6, S.8, D.181 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.7, A:S.8 PEG.9: 5 residues within 4Å: Chain B: S.208, S.211, T.213, S.268, E.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.208, B:T.213 PEG.12: 4 residues within 4Å: Chain C: L.53, Y.54 Chain E: Y.54, E.112 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.51, C:L.53 Water bridges: C:Y.54 PEG.13: 7 residues within 4Å: Chain C: N.188, F.189, H.190, K.274, Y.276, F.322, F.335 No protein-ligand interaction detected (PLIP) PEG.14: 3 residues within 4Å: Chain C: T.6, S.8, D.181 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.7, C:S.8 PEG.18: 5 residues within 4Å: Chain D: S.208, S.211, T.213, S.268, E.275 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.208 PEG.21: 4 residues within 4Å: Chain A: Y.54, E.112 Chain E: L.53, Y.54 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.51, E:L.53 PEG.22: 7 residues within 4Å: Chain E: N.188, F.189, H.190, K.274, Y.276, F.322, F.335 No protein-ligand interaction detected (PLIP) PEG.23: 3 residues within 4Å: Chain E: T.6, S.8, D.181 2 PLIP interactions: 2 interactions with chain E Water bridges: E:S.7, E:S.8 PEG.27: 5 residues within 4Å: Chain F: S.208, S.211, T.213, S.268, E.275 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.208

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

PGE.8: 6 residues within 4Å: Chain B: L.194, I.195, K.196, R.329, N.330, N.331 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.329 PGE.17: 6 residues within 4Å: Chain D: L.194, I.195, K.196, R.329, N.330, N.331 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.329 PGE.26: 6 residues within 4Å: Chain F: L.194, I.195, K.196, R.329, N.330, N.331 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.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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