SMTL ID : 5uoc.2 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain in complex with (S)-3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-(2-(methylamino)propyl)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: 17 residues within 4Å: Chain A: W.138, A.141, R.143, C.144, S.186, M.299, F.313, S.314, G.315, W.316, M.318, E.321, W.407, F.433, Y.435 Ligands: H4B.2, 8FD.3 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, A:F.433 Salt bridges: A:R.143 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.12: 17 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, V.145, F.313, S.314, G.315, W.316, M.318, E.321, R.325, W.407, F.433, Y.435 Ligands: H4B.13, 8FD.14 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:A.141, B:F.313, B:F.313, B:F.313, B:W.316, B:E.321, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:Y.435 Salt bridges: B:R.143, B:R.325 pi-Stacking: B:W.138 Metal complexes: B:C.144

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

H4B.2: 12 residues within 4Å: Chain A: S.62, V.64, R.325, A.406, W.407 Chain B: W.405, F.420, H.421, Q.422, E.423 Ligands: HEM.1, 8FD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.325, A:A.406, A:W.407 pi-Stacking: A:W.407 H4B.13: 11 residues within 4Å: Chain A: W.34, W.405, F.420, H.421, Q.422 Chain B: S.62, V.64, A.406, W.407 Ligands: HEM.12, 8FD.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.64 Hydrogen bonds: B:A.406, B:W.407 pi-Stacking: B:W.407

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

8FD.3: 15 residues within 4Å: Chain A: P.294, V.296, N.298, M.299, F.313, S.314, G.315, W.316, Y.317, M.318, E.321, W.407, Y.435 Ligands: HEM.1, H4B.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.296, A:F.313, A:W.407, A:Y.435 Hydrogen bonds: A:N.298, A:W.316, A:M.318 8FD.14: 12 residues within 4Å: Chain B: V.296, F.313, G.315, W.316, Y.317, M.318, E.321, R.325, W.407, Y.435 Ligands: HEM.12, H4B.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.296, B:F.313, B:F.313, B:W.407 Hydrogen bonds: B:W.316, B:M.318

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

BTB.4: 3 residues within 4Å: Chain A: C.342, D.344 Ligands: GD.10 No protein-ligand interaction detected (PLIP) BTB.5: 2 residues within 4Å: Chain A: E.337, T.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.337 Salt bridges: A:E.337 BTB.6: 1 residues within 4Å: Chain A: E.258 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.258 BTB.15: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.279, B:E.281 Salt bridges: B:E.281 BTB.16: 3 residues within 4Å: Chain B: D.257, E.258, P.259 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.258

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: C.54, C.59, G.61 Chain B: C.54, C.59, L.60 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.54, A:C.59, B:C.54, B:C.59 ZN.11: 3 residues within 4Å: Chain A: H.421 Chain B: R.325, D.329 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.329, B:D.329, A:H.421, H2O.1, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: E.127 No protein-ligand interaction detected (PLIP)

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

CL.9: 4 residues within 4Å: Chain A: Q.207, R.210, Y.317, N.326 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, R.325, N.326 Ligand excluded by PLIP

2 x GD: GADOLINIUM ATOM(Non-covalent)

GD.10: 2 residues within 4Å: Chain A: D.344 Ligands: BTB.4 No protein-ligand interaction detected (PLIP) GD.17: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, B:E.281, H2O.1

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
C

B
D

Nitric oxide synthase, endothelial

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