SMTL ID : 5uod.1

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 3-[(2-Amino-4-methylquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: W.141, A.144, R.146, C.147, V.148, G.149, L.156, S.189, M.302, F.316, S.317, G.318, W.319, M.321, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.2, 8EY.3 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:W.141, A:W.141, A:W.141, A:A.144, A:R.146, A:L.156, A:F.316, A:F.316, A:F.316, A:W.319, A:W.319, A:E.324, A:V.381, A:W.410, A:W.410, A:F.436, A:F.436, A:F.436 Hydrogen bonds: A:Y.438 Water bridges: A:E.324, A:R.328 Salt bridges: A:R.146 pi-Stacking: A:W.141 Metal complexes: A:C.147 HEM.6: 21 residues within 4Å: Chain B: W.141, A.144, R.146, C.147, V.148, G.149, L.156, S.189, M.302, F.316, S.317, G.318, W.319, M.321, E.324, V.381, W.410, F.436, Y.438 Ligands: H4B.7, 8EY.8 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:W.141, B:W.141, B:W.141, B:A.144, B:R.146, B:L.156, B:F.316, B:F.316, B:F.316, B:W.319, B:E.324, B:V.381, B:W.410, B:F.436, B:F.436, B:F.436 Water bridges: B:R.328 Salt bridges: B:R.146 pi-Stacking: B:W.141 Metal complexes: B:C.147

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 12 residues within 4Å: Chain A: S.65, V.67, R.328, A.409, W.410 Chain B: W.408, F.423, H.424, Q.425, E.426 Ligands: HEM.1, GOL.4 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:E.426 Hydrogen bonds: A:R.328, A:A.409, A:W.410 Water bridges: A:S.65, A:W.410 pi-Stacking: A:W.410, A:W.410 pi-Cation interactions: A:W.410, A:W.410 H4B.7: 12 residues within 4Å: Chain A: W.408, F.423, H.424, Q.425, E.426 Chain B: S.65, V.67, R.328, A.409, W.410 Ligands: HEM.6, GOL.9 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:E.426 Hydrogen bonds: B:R.328, B:A.409, B:W.410 Water bridges: B:S.65, B:W.410 pi-Stacking: B:W.410, B:W.410 pi-Cation interactions: B:W.410

2 x 8EY: 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile(Non-covalent)

8EY.3: 14 residues within 4Å: Chain A: P.297, V.299, N.301, M.302, F.316, S.317, G.318, W.319, Y.320, M.321, E.324, Y.438 Ligands: HEM.1, GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.297, A:V.299, A:F.316, A:Y.438 Hydrogen bonds: A:N.301, A:M.321, A:E.324 8EY.8: 14 residues within 4Å: Chain B: P.297, V.299, N.301, M.302, F.316, S.317, G.318, W.319, Y.320, M.321, E.324, Y.438 Ligands: HEM.6, GOL.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.297, B:V.299, B:V.299, B:F.316, B:Y.438 Hydrogen bonds: B:N.301, B:M.321, B:E.324

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: V.67, R.328, H.334, W.410 Chain B: W.37 Ligands: H4B.2, 8EY.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.328, A:R.328, A:H.334 GOL.9: 7 residues within 4Å: Chain A: W.37 Chain B: V.67, R.328, H.334, W.410 Ligands: H4B.7, 8EY.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.328, B:R.328, B:H.334 Water bridges: A:H.424

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.57, C.62 Chain B: C.57, C.62 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.57, A:C.62, B:C.57, B:C.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cinelli, M.A. et al., Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. J. Med. Chem. (2017)

Release Date

2017-05-03

Peptides

Nitric oxide synthase, endothelial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, endothelial

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