SMTL ID : 3vsx.3 (2 other biounits)

Human renin in complex with compound 18

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75 NAG.3: 2 residues within 4Å: Chain B: N.75, T.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.77 NAG.5: 2 residues within 4Å: Chain C: N.75, M.107 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.75 NAG.7: 2 residues within 4Å: Chain D: N.75, T.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.77, D:T.77 NAG.9: 2 residues within 4Å: Chain E: N.75, M.107 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.75 NAG.11: 2 residues within 4Å: Chain F: N.75, T.77 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.77, F:T.77

6 x R32: (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-2-(propan-2-yl)hexanamide(Non-covalent)

R32.2: 19 residues within 4Å: Chain A: Q.19, V.36, D.38, G.40, S.41, R.82, Y.83, S.84, T.85, P.118, F.119, A.122, F.124, V.127, Q.135, L.224, D.226, G.228, I.305 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.19, A:V.36, A:D.38, A:A.122, A:L.224, A:I.305 Hydrogen bonds: A:D.38, A:D.38, A:G.40, A:S.84, A:Q.135 Salt bridges: A:D.38 pi-Stacking: A:F.124 R32.4: 21 residues within 4Å: Chain B: T.18, Q.19, V.36, D.38, G.40, S.41, R.82, Y.83, S.84, T.85, P.118, F.119, F.124, V.127, Q.135, I.137, L.224, D.226, G.228, S.230, I.305 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Q.19, B:V.36, B:D.38, B:V.127, B:V.127, B:I.137, B:L.224, B:I.305, B:I.305 Hydrogen bonds: B:D.38, B:D.38, B:G.40, B:S.42, B:S.84, B:T.85, B:Q.135 Salt bridges: B:D.38 pi-Stacking: B:F.124 R32.6: 19 residues within 4Å: Chain C: Q.19, V.36, D.38, G.40, S.41, R.82, Y.83, S.84, T.85, P.118, F.119, A.122, F.124, V.127, Q.135, L.224, D.226, G.228, I.305 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Q.19, C:V.36, C:D.38, C:A.122, C:L.224, C:I.305 Hydrogen bonds: C:D.38, C:D.38, C:G.40, C:S.84, C:Q.135 Salt bridges: C:D.38 pi-Stacking: C:F.124 R32.8: 21 residues within 4Å: Chain D: T.18, Q.19, V.36, D.38, G.40, S.41, R.82, Y.83, S.84, T.85, P.118, F.119, F.124, V.127, Q.135, I.137, L.224, D.226, G.228, S.230, I.305 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Q.19, D:V.36, D:D.38, D:V.127, D:V.127, D:I.137, D:L.224, D:I.305, D:I.305 Hydrogen bonds: D:D.38, D:D.38, D:G.40, D:S.42, D:S.84, D:T.85, D:Q.135 Salt bridges: D:D.38 pi-Stacking: D:F.124 R32.10: 19 residues within 4Å: Chain E: Q.19, V.36, D.38, G.40, S.41, R.82, Y.83, S.84, T.85, P.118, F.119, A.122, F.124, V.127, Q.135, L.224, D.226, G.228, I.305 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Q.19, E:V.36, E:D.38, E:A.122, E:L.224, E:I.305 Hydrogen bonds: E:D.38, E:D.38, E:G.40, E:S.84, E:Q.135 Salt bridges: E:D.38 pi-Stacking: E:F.124 R32.12: 21 residues within 4Å: Chain F: T.18, Q.19, V.36, D.38, G.40, S.41, R.82, Y.83, S.84, T.85, P.118, F.119, F.124, V.127, Q.135, I.137, L.224, D.226, G.228, S.230, I.305 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:Q.19, F:V.36, F:D.38, F:V.127, F:V.127, F:I.137, F:L.224, F:I.305, F:I.305 Hydrogen bonds: F:D.38, F:D.38, F:G.40, F:S.42, F:S.84, F:Q.135 Salt bridges: F:D.38 pi-Stacking: F:F.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, Y. et al., Design and optimization of novel (2S,4S,5S)-5-amino-6-(2,2-dimethyl-5-oxo-4-phenylpiperazin-1-yl)-4-hydroxy-2-isopropylhexanamides as renin inhibitors. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-07-25

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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