SMTL ID : 3sfc.5 (4 other biounits)

Structure-Based Optimization of Potent 4- and 6-Azaindole-3-Carboxamides as Renin Inhibitors

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: 2 residues within 4Å: Chain A: N.75, M.107 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.75, A:N.75 NAG.7: 2 residues within 4Å: Chain B: N.75, M.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.77, B:T.77 NAG.10: 2 residues within 4Å: Chain C: N.75, M.107 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.75, C:N.75 NAG.16: 2 residues within 4Å: Chain D: N.75, M.107 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.77 Water bridges: D:T.77, D:T.77 NAG.19: 2 residues within 4Å: Chain E: N.75, M.107 2 PLIP interactions: 2 interactions with chain E Water bridges: E:N.75, E:N.75 NAG.25: 2 residues within 4Å: Chain F: N.75, M.107 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.77 Water bridges: F:T.77, F:T.77

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: D.17, A.282, D.283, Y.284, V.285, F.286, A.299, T.318, R.321 Chain B: S.169, Q.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.321 Water bridges: A:Q.287 GOL.3: 12 residues within 4Å: Chain A: T.18, Q.19, Y.20, V.36, F.124, Y.162, T.227, G.228, A.229, S.230, A.317 Ligands: S53.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.20, A:Y.20, A:Y.162, A:A.229 Water bridges: A:F.37 GOL.4: 3 residues within 4Å: Chain A: K.50, G.76, F.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.50, A:G.76 GOL.8: 8 residues within 4Å: Chain B: D.17, A.282, D.283, V.285, F.286, A.299, T.318, R.321 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.282, B:R.321 Water bridges: B:R.164, B:Q.287, B:Q.287 GOL.11: 11 residues within 4Å: Chain C: D.17, A.282, D.283, Y.284, V.285, F.286, A.299, T.318, R.321 Chain D: S.169, Q.170 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.321 Water bridges: C:Q.287 GOL.12: 12 residues within 4Å: Chain C: T.18, Q.19, Y.20, V.36, F.124, Y.162, T.227, G.228, A.229, S.230, A.317 Ligands: S53.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.20, C:Y.20, C:Y.162, C:A.229 Water bridges: C:F.37 GOL.13: 3 residues within 4Å: Chain C: K.50, G.76, F.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.50, C:G.76 GOL.17: 8 residues within 4Å: Chain D: D.17, A.282, D.283, V.285, F.286, A.299, T.318, R.321 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.282, D:R.321 Water bridges: D:R.164, D:Q.287, D:Q.287 GOL.20: 11 residues within 4Å: Chain E: D.17, A.282, D.283, Y.284, V.285, F.286, A.299, T.318, R.321 Chain F: S.169, Q.170 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.17, E:R.321 Water bridges: E:Q.287 GOL.21: 12 residues within 4Å: Chain E: T.18, Q.19, Y.20, V.36, F.124, Y.162, T.227, G.228, A.229, S.230, A.317 Ligands: S53.23 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.20, E:Y.20, E:A.229 Water bridges: E:F.37 GOL.22: 3 residues within 4Å: Chain E: K.50, G.76, F.91 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.50, E:G.76 GOL.26: 8 residues within 4Å: Chain F: D.17, A.282, D.283, V.285, F.286, A.299, T.318, R.321 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:A.282, F:R.321 Water bridges: F:R.164, F:Q.287, F:Q.287

9 x S53: [7-benzyl-2-(5-fluoro-2-methylphenoxy)-1-phenyl-1H-pyrrolo[2,3-c]pyridin-3-yl](piperazin-1-yl)methanone(Non-covalent)

S53.5: 21 residues within 4Å: Chain A: Q.19, V.36, D.38, Y.83, S.84, T.85, P.118, F.119, L.121, A.122, F.124, V.127, D.226, G.228, A.229, S.230, H.301, M.303 Chain C: Y.60 Ligands: GOL.3, S53.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.19, A:Y.83, A:Y.83, A:Y.83, A:T.85, A:P.118, A:P.118, A:F.119, A:L.121, A:A.122, A:V.127 Hydrogen bonds: A:S.84, A:T.85, A:D.226 Water bridges: A:Y.231 pi-Stacking: A:F.124 S53.6: 11 residues within 4Å: Chain A: L.117, L.121, R.251, L.252, F.253 Chain C: Y.60, M.120, L.121 Ligands: S53.5, S53.15, S53.24 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.117, A:L.117, A:L.121, A:L.121, A:L.252, A:F.253, A:F.253, C:L.121 pi-Stacking: A:F.253 S53.9: 13 residues within 4Å: Chain B: Q.19, V.36, D.38, Y.83, S.84, T.85, P.118, F.119, V.127, D.226, G.228, A.229, S.230 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.19, B:Y.83, B:Y.83, B:T.85, B:T.85, B:P.118, B:F.119, B:V.127 Hydrogen bonds: B:S.84, B:T.85, B:D.226 Water bridges: B:S.230 S53.14: 21 residues within 4Å: Chain C: Q.19, V.36, D.38, Y.83, S.84, T.85, P.118, F.119, L.121, A.122, F.124, V.127, D.226, G.228, A.229, S.230, H.301, M.303 Chain E: Y.60 Ligands: GOL.12, S53.15 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:Q.19, C:Y.83, C:Y.83, C:Y.83, C:T.85, C:P.118, C:P.118, C:F.119, C:L.121, C:A.122, C:V.127 Hydrogen bonds: C:S.84, C:T.85, C:D.226 Water bridges: C:Y.231 pi-Stacking: C:F.124 S53.15: 11 residues within 4Å: Chain C: L.117, L.121, R.251, L.252, F.253 Chain E: Y.60, M.120, L.121 Ligands: S53.6, S53.14, S53.24 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:L.117, C:L.117, C:L.121, C:L.121, C:L.252, C:F.253, C:F.253, E:L.121 pi-Stacking: C:F.253 S53.18: 13 residues within 4Å: Chain D: Q.19, V.36, D.38, Y.83, S.84, T.85, P.118, F.119, V.127, D.226, G.228, A.229, S.230 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Q.19, D:Y.83, D:Y.83, D:T.85, D:T.85, D:P.118, D:F.119, D:V.127 Hydrogen bonds: D:S.84, D:T.85, D:D.226 Water bridges: D:S.230 S53.23: 21 residues within 4Å: Chain A: Y.60 Chain E: Q.19, V.36, D.38, Y.83, S.84, T.85, P.118, F.119, L.121, A.122, F.124, V.127, D.226, G.228, A.229, S.230, H.301, M.303 Ligands: GOL.21, S53.24 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:Q.19, E:Y.83, E:Y.83, E:Y.83, E:T.85, E:P.118, E:P.118, E:F.119, E:L.121, E:A.122, E:V.127 Hydrogen bonds: E:S.84, E:T.85, E:D.226 Water bridges: E:Y.231 pi-Stacking: E:F.124 S53.24: 11 residues within 4Å: Chain A: Y.60, M.120, L.121 Chain E: L.117, L.121, R.251, L.252, F.253 Ligands: S53.6, S53.15, S53.23 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.117, E:L.117, E:L.121, E:L.121, E:L.252, E:F.253, E:F.253, A:L.121 pi-Stacking: E:F.253 S53.27: 13 residues within 4Å: Chain F: Q.19, V.36, D.38, Y.83, S.84, T.85, P.118, F.119, V.127, D.226, G.228, A.229, S.230 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:Q.19, F:Y.83, F:Y.83, F:T.85, F:T.85, F:P.118, F:F.119, F:V.127 Hydrogen bonds: F:S.84, F:T.85, F:D.226 Water bridges: F:S.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scheiper, B. et al., Structure-based optimization of potent 4- and 6-azaindole-3-carboxamides as renin inhibitors. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-08-31

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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