SMTL ID : 5t4s.3 (2 other biounits)

Novel Approach of Fragment-Based Lead Discovery applied to Renin Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 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: H.73, N.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.74 NAG.5: 2 residues within 4Å: Chain B: N.74, M.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.74 NAG.8: 2 residues within 4Å: Chain C: H.73, N.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.74 NAG.12: 2 residues within 4Å: Chain D: N.74, M.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.74 NAG.15: 2 residues within 4Å: Chain E: H.73, N.74 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.74 NAG.19: 2 residues within 4Å: Chain F: N.74, M.106 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.74

3 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.2: 13 residues within 4Å: Chain A: Q.18, V.35, D.37, Y.82, T.84, P.117, F.118, L.120, F.123, V.126, G.227, F.252 Chain E: Y.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.84 Water bridges: A:T.84 PG6.9: 13 residues within 4Å: Chain A: Y.59 Chain C: Q.18, V.35, D.37, Y.82, T.84, P.117, F.118, L.120, F.123, V.126, G.227, F.252 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.84 Water bridges: C:T.84 PG6.16: 13 residues within 4Å: Chain C: Y.59 Chain E: Q.18, V.35, D.37, Y.82, T.84, P.117, F.118, L.120, F.123, V.126, G.227, F.252 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.84 Water bridges: E:T.84

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

DMS.3: 8 residues within 4Å: Chain A: T.17, Q.18, Y.19, V.35, T.226, G.227, A.228, S.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.19 DMS.4: 6 residues within 4Å: Chain A: D.16, A.281, D.282, V.284, F.285, R.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.16, A:R.320 Salt bridges: A:D.16 pi-Cation interactions: A:F.285 DMS.10: 8 residues within 4Å: Chain C: T.17, Q.18, Y.19, V.35, T.226, G.227, A.228, S.229 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.19 DMS.11: 6 residues within 4Å: Chain C: D.16, A.281, D.282, V.284, F.285, R.320 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.320 Salt bridges: C:D.16 pi-Cation interactions: C:F.285 DMS.17: 8 residues within 4Å: Chain E: T.17, Q.18, Y.19, V.35, T.226, G.227, A.228, S.229 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.19 DMS.18: 6 residues within 4Å: Chain E: D.16, A.281, D.282, V.284, F.285, R.320 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.16, E:R.320 Salt bridges: E:D.16 pi-Cation interactions: E:F.285

3 x 77O: 6-chloro-N-[(furan-2-yl)methyl]pyrazin-2-amine(Non-covalent)

77O.6: 11 residues within 4Å: Chain B: T.17, Q.18, Y.19, V.35, P.117, F.118, F.123, T.226, G.227, A.228, S.229 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.35, B:V.35 Hydrogen bonds: B:G.227 Water bridges: B:Q.18, B:S.229 77O.13: 11 residues within 4Å: Chain D: T.17, Q.18, Y.19, V.35, P.117, F.118, F.123, T.226, G.227, A.228, S.229 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.35, D:V.35 Hydrogen bonds: D:G.227 Water bridges: D:Q.18, D:S.229 77O.20: 11 residues within 4Å: Chain F: T.17, Q.18, Y.19, V.35, P.117, F.118, F.123, T.226, G.227, A.228, S.229 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.35, F:V.35 Hydrogen bonds: F:G.227 Water bridges: F:Q.18, F:S.229

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

PGE.7: 4 residues within 4Å: Chain B: L.194, R.329, N.330, N.331 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.331 PGE.14: 4 residues within 4Å: Chain D: L.194, R.329, N.330, N.331 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.331 PGE.21: 4 residues within 4Å: Chain F: L.194, R.329, N.330, N.331 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tawada, M. et al., Novel approach of fragment-based lead discovery applied to renin inhibitors. Bioorg.Med.Chem. (2016)

Release Date

2016-10-26

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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