SMTL ID : 4d3n.1

Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)-5-((2-(pyridin-2-yl)ethyl)amino)benzonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 20 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, L.75, P.108, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: SK6.2, GOL.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:W.60, A:W.60, A:W.60, A:R.65, A:I.67, A:L.75, A:P.108, A:F.235, A:F.235, A:F.235, A:W.238, A:W.238, A:E.243, A:V.300, A:W.329, A:Y.355, A:Y.355 Salt bridges: A:R.65 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.9: 20 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, L.75, P.108, M.221, F.235, N.236, G.237, W.238, M.240, E.243, V.300, W.329, Y.355, Y.357 Ligands: SK6.10, GOL.11 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:W.60, B:W.60, B:W.60, B:R.65, B:I.67, B:L.75, B:P.108, B:F.235, B:F.235, B:F.235, B:W.238, B:W.238, B:E.243, B:V.300, B:W.329, B:Y.355, B:Y.355 Salt bridges: B:R.65 pi-Stacking: B:W.60 Metal complexes: B:C.66

2 x SK6: 3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{[2-(pyridin-2-yl)ethyl]amino}benzonitrile(Non-covalent)

SK6.2: 16 residues within 4Å: Chain A: H.128, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, T.328, W.329, Y.357 Chain B: F.342 Ligands: HEM.1, POL.4, POL.8 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.216, A:I.218, A:I.218, A:F.235, A:W.329, B:F.342 Hydrogen bonds: A:M.240, A:E.243 Water bridges: A:R.247, A:Y.357 pi-Stacking: A:W.329 SK6.10: 16 residues within 4Å: Chain A: F.342 Chain B: H.128, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, T.328, W.329, Y.357 Ligands: HEM.9, POL.12, POL.16 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.216, B:I.218, B:I.218, B:F.235, B:W.329, A:F.342 Hydrogen bonds: B:M.240, B:E.243 Water bridges: B:R.247, B:Y.357 pi-Stacking: B:W.329

6 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: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.357 Water bridges: A:N.354 GOL.5: 5 residues within 4Å: Chain A: W.238, S.298, I.299, V.300, Q.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.298, A:I.299, A:Q.308 GOL.6: 7 residues within 4Å: Chain A: R.142, I.143, G.144, D.166, R.254, Y.255, K.257 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.142, A:G.144, A:D.166, A:R.254, A:K.257, A:K.257 Water bridges: A:R.142, A:D.166 GOL.11: 6 residues within 4Å: Chain B: R.65, M.221, Y.355, F.356, Y.357 Ligands: HEM.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.357 Water bridges: B:N.354 GOL.13: 5 residues within 4Å: Chain B: W.238, S.298, I.299, V.300, Q.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.298, B:I.299, B:Q.308 GOL.14: 7 residues within 4Å: Chain B: R.142, I.143, G.144, D.166, R.254, Y.255, K.257 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.142, B:G.144, B:D.166, B:R.254, B:K.257, B:K.257 Water bridges: B:R.142, B:D.166

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

POL.4: 5 residues within 4Å: Chain A: E.243, R.247, N.248, R.254 Ligands: SK6.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.247 Water bridges: A:N.248, A:N.248 POL.7: 6 residues within 4Å: Chain A: P.196, I.197, T.198, S.206, E.209, L.210 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.196 Water bridges: A:L.210 POL.8: 5 residues within 4Å: Chain A: T.328, W.329 Chain B: W.327, R.344 Ligands: SK6.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.327, A:T.328 Hydrogen bonds: A:T.328, A:W.329 POL.12: 5 residues within 4Å: Chain B: E.243, R.247, N.248, R.254 Ligands: SK6.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.247 Water bridges: B:N.248, B:N.248 POL.15: 6 residues within 4Å: Chain B: P.196, I.197, T.198, S.206, E.209, L.210 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.196 Water bridges: B:L.210 POL.16: 5 residues within 4Å: Chain A: W.327, R.344 Chain B: T.328, W.329 Ligands: SK6.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.328, A:W.327 Hydrogen bonds: B:T.328, B:W.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holden, J.K. et al., Structure-based design of bacterial nitric oxide synthase inhibitors. J. Med. Chem. (2015)

Release Date

2015-01-14

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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