SMTL ID : 4d3m.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: W.60, S.63, R.65, C.66, I.67, F.235, N.236, G.237, W.238, M.240, E.243, R.247, V.300, W.329, Y.355, Y.357 Ligands: IVU.3 18 PLIP interactions: 18 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 Water bridges: A:R.65, A:R.247 Salt bridges: A:R.65, A:R.247 pi-Stacking: A:W.60 Metal complexes: A:C.66 HEM.7: 17 residues within 4Å: Chain B: W.60, S.63, R.65, C.66, I.67, F.235, N.236, G.237, W.238, M.240, E.243, R.247, V.300, W.329, Y.355, Y.357 Ligands: IVU.9 18 PLIP interactions: 18 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 Water bridges: B:R.65, B:R.247 Salt bridges: B:R.65, B:R.247 pi-Stacking: B:W.60 Metal complexes: B:C.66

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

CL.2: 6 residues within 4Å: Chain A: Q.129, Y.213, Y.239, R.247, N.248 Ligands: IVU.3 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: Q.129, Y.213, Y.239, R.247, N.248 Ligands: IVU.9 Ligand excluded by PLIP

2 x IVU: 3-[2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL]-5-{2-[4-METHYL-6-(METHYLAMINO)PYRIDIN-2-YL]ETHYL}BENZONITRILE(Non-covalent)

IVU.3: 18 residues within 4Å: Chain A: H.128, Q.129, R.132, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, N.248, R.254, T.328, W.329 Chain B: F.342 Ligands: HEM.1, CL.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.218, A:I.218, A:F.235, A:W.329, A:W.329 Hydrogen bonds: A:Q.129, A:R.132, A:E.243, A:R.247, A:R.254, A:R.254 pi-Stacking: A:W.329 pi-Cation interactions: A:R.247 IVU.9: 18 residues within 4Å: Chain A: F.342 Chain B: H.128, Q.129, R.132, P.216, I.218, F.235, G.237, W.238, Y.239, E.243, R.247, N.248, R.254, T.328, W.329 Ligands: HEM.7, CL.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.218, B:I.218, B:F.235, B:W.329, B:W.329 Hydrogen bonds: B:Q.129, B:R.132, B:E.243, B:R.247, B:R.254, B:R.254 pi-Stacking: B:W.329 pi-Cation interactions: B:R.247

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

POL.4: 2 residues within 4Å: Chain A: V.183, W.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.184 Water bridges: A:P.182, A:W.184 POL.6: 5 residues within 4Å: Chain A: K.310, E.313, E.314, E.317, R.344 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.313, A:E.314 Hydrogen bonds: A:K.310, A:K.310 Water bridges: A:R.344 POL.10: 2 residues within 4Å: Chain B: V.183, W.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.184 Water bridges: B:P.182, B:W.184 POL.12: 5 residues within 4Å: Chain B: K.310, E.313, E.314, E.317, R.344 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.313, B:E.314 Hydrogen bonds: B:K.310, B:K.310 Water bridges: B:R.344

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: W.238, S.298, I.299, V.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.238, A:S.298, A:I.299 GOL.11: 4 residues within 4Å: Chain B: W.238, S.298, I.299, V.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.238, B:S.298, B:I.299

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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