SMTL ID : 5vvb.1 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-Aminoquinolin-7-yl)methyl)amino)ethyl)-2-methylbenzonitrile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: W.138, A.141, R.143, C.144, V.145, G.146, 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, 9P7.3 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:W.138, A:A.141, A:R.143, A:V.145, A:F.313, A:F.313, A:F.313, A:W.316, A:E.321, A:F.433, A:F.433, A:F.433 Water bridges: A:R.325, A:R.325 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.10: 18 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, V.145, G.146, S.186, F.313, S.314, G.315, W.316, E.321, V.378, W.407, F.433, Y.435 Ligands: H4B.11, 9P7.12 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:R.143, B:V.145, B:F.313, B:F.313, B:F.313, B:W.316, B:E.321, B:V.378, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:Y.435 Water bridges: 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: 10 residues within 4Å: Chain A: S.62, R.325, A.406, W.407 Chain B: W.405, F.420, H.421, Q.422, E.423 Ligands: HEM.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.325, A:R.325, A:A.406, A:W.407 pi-Stacking: A:W.407, A:W.407 Hydrophobic interactions: B:E.423 H4B.11: 11 residues within 4Å: Chain A: W.405, F.420, H.421, Q.422, E.423 Chain B: S.62, V.64, R.325, A.406, W.407 Ligands: HEM.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.325, B:R.325, B:A.406, B:W.407 pi-Stacking: B:W.407, B:W.407 Hydrophobic interactions: A:E.423

2 x 9P7: 4-(2-{[(2-aminoquinolin-7-yl)methyl]amino}ethyl)-2-methylbenzonitrile(Non-covalent)

9P7.3: 10 residues within 4Å: Chain A: V.64, F.65, V.296, F.313, W.316, E.321, W.407, Y.435 Chain B: W.34 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.64, A:F.65, A:V.296, A:W.407, A:Y.435 Hydrogen bonds: A:E.321 9P7.12: 12 residues within 4Å: Chain A: W.34 Chain B: V.64, F.65, P.294, V.296, F.313, W.316, Y.317, E.321, W.407, Y.435 Ligands: HEM.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.64, B:V.296, B:F.313, B:W.407 Hydrogen bonds: B:W.316

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

BTB.4: 5 residues within 4Å: Chain A: W.282, V.341, C.342, D.344 Ligands: GD.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.344 BTB.5: 2 residues within 4Å: Chain A: E.337, T.347 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.337 BTB.13: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.281 Water bridges: B:T.279, B:T.279 Salt bridges: B:E.281 BTB.14: 3 residues within 4Å: Chain B: D.257, E.258, P.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.257 Salt bridges: B:E.258 BTB.15: 2 residues within 4Å: Chain B: Q.49, Q.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.49, B:Q.82

1 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 A, 2 interactions with chain B Metal complexes: A:C.54, A:C.59, B:C.54, B:C.59

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.16: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, B:E.281, H2O.5

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

CL.9: 3 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: Q.207, R.210, Y.317, N.326 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pensa, A.V. et al., Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines as Improved Human Neuronal Nitric Oxide Synthase Inhibitors. J. Med. Chem. (2017)

Release Date

2017-08-16

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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