SMTL ID : 5uoa.1

Structure of human 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 2.20 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: W.138, A.141, R.143, C.144, V.145, G.146, S.186, F.313, S.314, G.315, W.316, M.318, E.321, R.325, W.407, F.433, Y.435 Ligands: 8EY.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:A.141, A:F.313, A:F.313, A:W.316, A:F.433, A:F.433 Salt bridges: A:R.143, A:R.325 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.12: 15 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, F.313, S.314, G.315, W.316, M.318, E.321, R.325, W.407, F.433, Y.435 Ligands: 8EY.13 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:R.143, B:F.313, B:F.313, B:F.313, B:W.316, B:E.321, B:F.433, B:F.433, B:F.433 Salt bridges: B:R.143, B:R.325 pi-Stacking: B:W.138 Metal complexes: B:C.144

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

8EY.2: 11 residues within 4Å: Chain A: P.294, V.296, N.298, G.315, W.316, Y.317, M.318, E.321, R.325, W.407 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.294, A:V.296 Hydrogen bonds: A:N.298, A:M.318, A:E.321 8EY.3: 10 residues within 4Å: Chain A: S.62, V.64, P.330, H.331, A.406, W.407 Chain B: W.34, W.405, F.420, H.421 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.34, B:W.405, A:V.64 pi-Stacking: B:H.421, A:W.407 Hydrogen bonds: A:H.331, A:H.331, A:A.406 8EY.13: 9 residues within 4Å: Chain B: P.294, V.296, G.315, W.316, Y.317, M.318, E.321, Y.435 Ligands: HEM.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.294, B:V.296, B:Y.435 Hydrogen bonds: B:W.316, B:M.318 8EY.14: 12 residues within 4Å: Chain A: W.34, E.35, W.405, F.420, H.421 Chain B: S.62, V.64, D.329, P.330, H.331, A.406, W.407 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.64, B:W.407, A:W.34, A:W.405 Hydrogen bonds: B:H.331, B:A.406 pi-Stacking: B:W.407

8 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 4 residues within 4Å: Chain A: W.282, C.342, D.344 Ligands: GD.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.344 BTB.5: 3 residues within 4Å: Chain A: E.337, T.347, R.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.347, A:R.348 Salt bridges: A:E.337 BTB.15: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.281 Water bridges: B:T.279 Salt bridges: B:E.281 BTB.16: 1 residues within 4Å: Chain B: E.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.337 Salt bridges: B:E.337 BTB.17: 1 residues within 4Å: Chain B: E.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.258 Salt bridges: B:E.258 BTB.18: 2 residues within 4Å: Chain B: D.344, L.345 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.344, B:D.344 Salt bridges: B:D.344 BTB.19: 3 residues within 4Å: Chain B: F.65, E.229, D.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.229 Salt bridges: B:E.229, B:D.438 BTB.20: 1 residues within 4Å: Chain B: D.160 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.160, B:D.160 Salt bridges: B:D.160

3 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.54, C.59 Chain B: C.54, C.59 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.54, B:C.59, A:C.54, A:C.59 ZN.9: 3 residues within 4Å: Chain A: H.421 Chain B: R.325, D.329 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.421, B:D.329, B:D.329, H2O.1, H2O.2 ZN.10: 3 residues within 4Å: Chain A: R.325, D.329 Chain B: H.421 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.421, A:D.329, H2O.1, H2O.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: E.127 No protein-ligand interaction detected (PLIP)

2 x GD: GADOLINIUM ATOM(Non-functional Binders)(Non-covalent)

GD.8: 1 residues within 4Å: Ligands: BTB.4 No protein-ligand interaction detected (PLIP) GD.21: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.2, H2O.2

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

CL.11: 6 residues within 4Å: Chain A: Q.207, R.210, Y.291, Y.317, R.325, N.326 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain B: Q.207, R.210, Y.317, R.325, N.326 Ligand excluded by PLIP

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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