SMTL ID : 6xcx.1

Nitric Oxide Synthase from Bacillus subtilis in complex with N2-((3-((2-aminoquinolin-7-yl)methoxy)phenoxy)methyl)pyridine-2,6-diamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Non-covalent)

HEC.1: 18 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: GOL.3, V0P.7 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:I.67, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:Y.355, A:Y.355 Water bridges: A:W.329 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEC.8: 18 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: GOL.10, V0P.14 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:I.67, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:Y.355, B:Y.355 Water bridges: B:W.329 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: Q.129, Y.213, Y.239, N.248 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: Q.129, Y.213, Y.239, N.248 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.357 GOL.10: 6 residues within 4Å: Chain B: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEC.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.357

4 x POL: N-PROPANOL(Non-covalent)

POL.4: 3 residues within 4Å: Chain A: W.238, S.298, I.299 No protein-ligand interaction detected (PLIP) POL.5: 6 residues within 4Å: Chain A: R.142, G.144, D.166, R.254, Y.255, K.257 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.142 Hydrogen bonds: A:K.257, A:K.257 Water bridges: A:D.166 POL.11: 3 residues within 4Å: Chain B: W.238, S.298, I.299 No protein-ligand interaction detected (PLIP) POL.12: 6 residues within 4Å: Chain B: R.142, G.144, D.166, R.254, Y.255, K.257 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.142 Hydrogen bonds: B:K.257, B:K.257 Water bridges: B:D.166

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

PEG.6: 6 residues within 4Å: Chain A: R.65, T.328, W.329 Chain B: W.327, S.345, Y.346 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.346, B:Y.346, A:R.65, A:T.328, A:W.329 Water bridges: B:W.327 PEG.13: 6 residues within 4Å: Chain A: W.327, S.345, Y.346 Chain B: R.65, T.328, W.329 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.65, B:T.328, B:W.329, A:Y.346, A:Y.346 Water bridges: A:W.327

2 x V0P: 7-{[3-(2-{[(6-aminopyridin-2-yl)methyl]amino}ethoxy)phenoxy]methyl}quinolin-2-amine(Non-covalent)

V0P.7: 11 residues within 4Å: Chain A: I.218, W.238, Y.239, E.243, R.247, T.328, W.329, Y.357 Chain B: W.327, F.342 Ligands: HEC.1 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.327, B:W.327, A:I.218, A:W.329 Hydrogen bonds: B:F.342, A:E.243, A:R.247 pi-Stacking: B:F.342, A:W.329 Water bridges: A:Q.129 V0P.14: 11 residues within 4Å: Chain A: W.327, F.342 Chain B: I.218, W.238, Y.239, E.243, R.247, T.328, W.329, Y.357 Ligands: HEC.8 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.218, B:W.329, A:W.327, A:W.327 Hydrogen bonds: B:E.243, B:R.247, A:F.342 Water bridges: B:Q.129 pi-Stacking: B:W.329, A:F.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, M.C. et al., Selective Anti-MRSA inhibitors targeting Nitric Oxide Synthase. To Be Published

Release Date

2021-06-16

Peptides

Nitric oxide synthase oxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitric oxide synthase oxygenase

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