SMTL ID : 6suk.1

Crystal structure of Neprilysin in complex with Omapatrilat.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.533, H.537, E.596, H.661 Ligands: FT8.6, EDO.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.533, A:H.537, A:E.596, A:E.596

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

NAG.2: 3 residues within 4Å: Chain A: N.94, A.97, D.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.94 NAG.3: 2 residues within 4Å: Chain A: N.234, K.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.234 Water bridges: A:K.303 NAG.4: 7 residues within 4Å: Chain A: T.132, K.135, K.268, N.274, N.277, E.278, S.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.277 Hydrogen bonds: A:N.274, A:E.278 NAG.5: 5 residues within 4Å: Chain A: Y.573, G.576, N.577, H.587, K.694 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.577

1 x FT8: Omapatrilat(Non-covalent)

FT8.6: 21 residues within 4Å: Chain A: R.52, F.56, R.60, N.492, A.493, I.508, F.513, M.529, V.530, H.533, E.534, H.537, E.596, V.642, W.643, Y.651, D.659, H.661, R.667 Ligands: ZN.1, EDO.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.56, A:I.508, A:F.513, A:V.530, A:W.643 Hydrogen bonds: A:N.492, A:N.492, A:R.667, A:R.667 Water bridges: A:R.52, A:R.52, A:R.60, A:R.60 Salt bridges: A:R.60 pi-Stacking: A:H.533

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

PEG.7: 7 residues within 4Å: Chain A: V.80, Q.83, K.84, A.87, L.449, N.450, Y.451 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.83, A:Y.451 Water bridges: A:Q.83 PEG.11: 6 residues within 4Å: Chain A: N.44, V.45, I.46, E.48, T.646, R.648 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.46, A:E.48, A:R.648, A:R.648 Water bridges: A:N.44, A:E.48

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: E.77, D.78, I.79, V.80, Q.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.77, A:Q.83 Water bridges: A:V.80 EDO.9: 8 residues within 4Å: Chain A: A.493, F.494, Y.495, E.534, H.537, E.596 Ligands: ZN.1, FT8.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.495 Water bridges: A:A.493, A:Y.495, A:D.540, A:N.542, A:E.596 EDO.10: 8 residues within 4Å: Chain A: N.370, P.432, D.434, I.435, K.441, D.482, E.483, W.484 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.370, A:D.434, A:K.441 EDO.12: 6 residues within 4Å: Chain A: D.158, P.245, S.497, G.498, N.542, F.546 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.497, A:G.498, A:N.542 Water bridges: A:D.158, A:S.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, U. et al., Molecular Basis for Omapatrilat and Sampatrilat Binding to Neprilysin-Implications for Dual Inhibitor Design with Angiotensin-Converting Enzyme. J.Med.Chem. (2020)

Release Date

2020-05-13

Peptides

Neprilysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neprilysin

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