SMTL ID : 5sy2.3 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-hexamer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: H.74, N.75, T.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75 NAG.6: 2 residues within 4Å: Chain B: N.75, T.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.75 NAG.9: 3 residues within 4Å: Chain C: H.74, N.75, T.77 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.75 NAG.14: 2 residues within 4Å: Chain D: N.75, T.77 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.75 NAG.17: 3 residues within 4Å: Chain E: H.74, N.75, T.77 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.75 NAG.22: 2 residues within 4Å: Chain F: N.75, T.77 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.75

6 x 74V: N-ethyl-4-{[(furan-2-yl)methyl]amino}-2-methyl-N-[(3S)-piperidin-3-yl]pyrimidine-5-carboxamide(Non-covalent)

74V.2: 17 residues within 4Å: Chain A: T.18, Q.19, Y.20, V.36, D.38, G.40, Y.83, T.85, P.118, F.124, V.127, Y.162, D.226, T.227, G.228, A.229, S.230 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.36, A:V.36, A:Y.83, A:Y.83, A:F.124, A:V.127 Hydrogen bonds: A:D.38, A:G.228 Water bridges: A:S.230, A:S.230 74V.7: 14 residues within 4Å: Chain B: T.18, Q.19, Y.20, V.36, D.38, G.40, L.121, F.124, Y.162, D.226, T.227, G.228, A.229, S.230 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.36, B:L.121 Hydrogen bonds: B:D.38, B:G.228 Water bridges: B:S.230, B:S.230 74V.10: 17 residues within 4Å: Chain C: T.18, Q.19, Y.20, V.36, D.38, G.40, Y.83, T.85, P.118, F.124, V.127, Y.162, D.226, T.227, G.228, A.229, S.230 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.36, C:V.36, C:Y.83, C:Y.83, C:F.124, C:V.127 Hydrogen bonds: C:D.38, C:G.228 Water bridges: C:S.230, C:S.230 74V.15: 14 residues within 4Å: Chain D: T.18, Q.19, Y.20, V.36, D.38, G.40, L.121, F.124, Y.162, D.226, T.227, G.228, A.229, S.230 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.36, D:L.121 Hydrogen bonds: D:D.38, D:G.228 Water bridges: D:S.230, D:S.230 74V.18: 17 residues within 4Å: Chain E: T.18, Q.19, Y.20, V.36, D.38, G.40, Y.83, T.85, P.118, F.124, V.127, Y.162, D.226, T.227, G.228, A.229, S.230 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:V.36, E:V.36, E:Y.83, E:Y.83, E:F.124, E:V.127 Hydrogen bonds: E:D.38, E:G.228 Water bridges: E:S.230, E:S.230 74V.23: 14 residues within 4Å: Chain F: T.18, Q.19, Y.20, V.36, D.38, G.40, L.121, F.124, Y.162, D.226, T.227, G.228, A.229, S.230 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:V.36, F:L.121 Hydrogen bonds: F:D.38, F:G.228 Water bridges: F:S.230, F:S.230

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

PGE.3: 7 residues within 4Å: Chain A: F.132, L.195, I.196, K.197, T.198, G.199, N.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.198, A:G.199 PGE.11: 7 residues within 4Å: Chain C: F.132, L.195, I.196, K.197, T.198, G.199, N.332 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.198, C:G.199 PGE.19: 7 residues within 4Å: Chain E: F.132, L.195, I.196, K.197, T.198, G.199, N.332 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.198, E:G.199

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

DMS.4: 6 residues within 4Å: Chain A: D.17, A.282, D.283, V.285, F.286, R.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321 Salt bridges: A:D.17 pi-Cation interactions: A:F.286 DMS.5: 4 residues within 4Å: Chain A: S.84, M.303, D.304 Chain E: V.59 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A pi-Cation interactions: E:Y.60 Hydrogen bonds: A:D.304 DMS.12: 6 residues within 4Å: Chain C: D.17, A.282, D.283, V.285, F.286, R.321 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.17, C:R.321 Salt bridges: C:D.17 pi-Cation interactions: C:F.286 DMS.13: 4 residues within 4Å: Chain A: V.59 Chain C: S.84, M.303, D.304 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C pi-Cation interactions: A:Y.60 Hydrogen bonds: C:D.304 DMS.20: 6 residues within 4Å: Chain E: D.17, A.282, D.283, V.285, F.286, R.321 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.17, E:R.321 Salt bridges: E:D.17 pi-Cation interactions: E:F.286 DMS.21: 4 residues within 4Å: Chain C: V.59 Chain E: S.84, M.303, D.304 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:D.304 pi-Cation interactions: C:Y.60

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 6 residues within 4Å: Chain B: L.195, I.196, K.197, R.330, N.331, N.332 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.198, B:N.332, B:N.332 1PE.16: 6 residues within 4Å: Chain D: L.195, I.196, K.197, R.330, N.331, N.332 3 PLIP interactions: 3 interactions with chain D Water bridges: D:T.198, D:N.332, D:N.332 1PE.24: 6 residues within 4Å: Chain F: L.195, I.196, K.197, R.330, N.331, N.332 3 PLIP interactions: 3 interactions with chain F Water bridges: F:T.198, F:N.332, F:N.332

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

Related Entries With Identical Sequence