SMTL ID : 5sy3.1 (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 2.30 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.74, T.76, M.106, G.137, V.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.74, A:N.74, A:G.137

1 x 74Z: N-[(furan-2-yl)methyl]-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine(Non-covalent)

74Z.2: 19 residues within 4Å: Chain A: T.17, Q.18, Y.19, V.35, D.37, Y.82, T.84, P.117, F.118, L.120, F.123, V.126, Y.161, T.226, G.227, A.228, S.229 Ligands: DMS.4, DMS.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.35, A:Y.82, A:Y.82, A:V.126 Hydrogen bonds: A:G.227 pi-Stacking: A:F.123, A:F.123

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

DMS.3: 5 residues within 4Å: Chain A: E.154, V.156, D.327, R.329, N.330 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.154, A:D.327 DMS.4: 6 residues within 4Å: Chain A: T.17, Q.18, S.229, Y.230 Ligands: 74Z.2, DMS.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.18 DMS.5: 5 residues within 4Å: Chain A: T.84, A.228, S.229 Ligands: 74Z.2, DMS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.229 Water bridges: A:Y.230 DMS.6: 4 residues within 4Å: Chain A: P.29, Q.30, T.31, K.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.31, A:K.61 DMS.7: 2 residues within 4Å: Chain A: Y.14, E.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.14 Salt bridges: A:E.122 DMS.10: 3 residues within 4Å: Chain A: V.9, I.10, E.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.10 Salt bridges: A:E.22

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

PEG.8: 5 residues within 4Å: Chain A: S.208, S.211, D.266, S.268, E.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.208, A:S.208, A:D.266, A:D.266, A:S.268

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

1PE.9: 8 residues within 4Å: Chain A: L.194, I.195, K.196, T.197, R.328, R.329, N.330, N.331 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.197, A:N.331, A:N.331, A: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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Renin

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