SMTL ID : 5sxn.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 2.10 Å

Oligo State

homo-hexamer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: H.73, N.74, T.76 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: H.73, N.74, T.76 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: H.73, N.74, T.76 No protein-ligand interaction detected (PLIP)

3 x 74U: N-[(furan-2-yl)methyl]-2-phenylquinazolin-4-amine(Non-covalent)

74U.2: 18 residues within 4Å: Chain A: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, P.117, L.120, A.121, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 Ligands: PEG.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.19, A:V.35, A:Y.82, A:Y.82, A:P.117, A:L.120, A:A.121, A:V.126 Hydrogen bonds: A:G.227 pi-Stacking: A:F.123 74U.8: 18 residues within 4Å: Chain C: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, P.117, L.120, A.121, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 Ligands: PEG.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.19, C:V.35, C:Y.82, C:Y.82, C:P.117, C:L.120, C:A.121, C:V.126 Hydrogen bonds: C:G.227 pi-Stacking: C:F.123 74U.14: 18 residues within 4Å: Chain E: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, P.117, L.120, A.121, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 Ligands: PEG.15 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.19, E:V.35, E:Y.82, E:Y.82, E:P.117, E:L.120, E:A.121, E:V.126 Hydrogen bonds: E:G.227 pi-Stacking: E:F.123

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

PEG.3: 2 residues within 4Å: Chain A: F.252 Ligands: 74U.2 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.59 PEG.5: 8 residues within 4Å: Chain A: S.208, S.268, E.275, T.277 Chain B: P.29, Q.30, T.31, K.61 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.208, A:S.208, A:S.268, B:T.31, B:T.31, B:T.31, B:K.61 PEG.9: 2 residues within 4Å: Chain C: F.252 Ligands: 74U.8 1 PLIP interactions: 1 interactions with chain E Water bridges: E:Y.59 PEG.11: 8 residues within 4Å: Chain C: S.208, S.268, E.275, T.277 Chain D: P.29, Q.30, T.31, K.61 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.31, D:T.31, D:K.61, C:S.208, C:S.208, C:S.268 PEG.15: 2 residues within 4Å: Chain E: F.252 Ligands: 74U.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.59 PEG.17: 8 residues within 4Å: Chain E: S.208, S.268, E.275, T.277 Chain F: P.29, Q.30, T.31, K.61 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:S.208, E:S.208, E:S.268, F:T.31, F:T.31, F:K.61

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain B: N.74, T.76, M.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.76, B:T.76 NAG.10: 3 residues within 4Å: Chain D: N.74, T.76, M.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.76 NAG.16: 3 residues within 4Å: Chain F: N.74, T.76, M.106 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.76, F:T.76

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

PGE.6: 6 residues within 4Å: Chain B: L.194, I.195, K.196, R.329, N.330, N.331 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.195 Water bridges: B:T.197, B:N.331, B:N.331 PGE.12: 6 residues within 4Å: Chain D: L.194, I.195, K.196, R.329, N.330, N.331 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.195 Water bridges: D:T.197, D:N.331, D:N.331 PGE.18: 6 residues within 4Å: Chain F: L.194, I.195, K.196, R.329, N.330, N.331 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:I.195 Water bridges: F:T.197, F:N.331, F:N.331

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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