SMTL ID : 9c1z.1 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain in complex with 7-((3-(((4-(6-aminopyridin-2-yl)butyl)amino)methyl)phenoxy)methyl)quinolin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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, S.186, M.299, F.313, S.314, G.315, W.316, M.318, E.321, V.378, W.407, F.433, Y.435 Ligands: V5D.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: 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:F.313, A:W.316, A:E.321, A:V.378, A:W.407, A:W.407, A:F.433, A:F.433, A:F.433 Hydrogen bonds: A:Y.435 Water bridges: A:E.321, A:R.325, A:R.325, A:R.325 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.12: 18 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, V.145, S.186, M.299, F.313, S.314, G.315, W.316, M.318, E.321, V.378, W.407, F.433, Y.435 Ligands: V5D.13 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:F.313, B:F.313, B:F.313, B:F.313, B:W.316, B:E.321, B:V.378, B:W.407, B:F.433, B:F.433, B:F.433 Water bridges: B:E.321, B:R.325, B:R.325 pi-Stacking: B:W.138 Metal complexes: B:C.144

2 x V5D: 7-{[3-({[4-(6-aminopyridin-2-yl)butyl]amino}methyl)phenoxy]methyl}quinolin-2-amine(Non-covalent)

V5D.2: 15 residues within 4Å: Chain A: V.64, Q.207, P.294, V.296, F.313, W.316, Y.317, E.321, R.325, A.406, W.407 Chain B: W.34, W.405, F.420 Ligands: HEM.1 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.64, A:V.64, A:P.294, A:V.296, A:F.313, A:W.407, B:W.34, B:W.405, B:F.420, B:F.420 Hydrogen bonds: A:W.316, A:M.318, A:R.325, A:R.325, A:A.406 pi-Stacking: A:W.407, B:W.34 V5D.13: 14 residues within 4Å: Chain A: W.34, W.405, F.420 Chain B: V.64, P.294, V.296, W.316, Y.317, M.318, E.321, R.325, A.406, W.407 Ligands: HEM.12 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:W.34, A:W.405, B:V.64, B:V.64, B:P.294, B:V.296, B:W.407 pi-Stacking: A:W.34, A:F.420, B:W.407 Hydrogen bonds: B:M.318, B:E.321, B:R.325, B:R.325, B:A.406

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

BTB.3: 5 residues within 4Å: Chain A: W.282, V.341, C.342, D.344 Ligands: GD.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.344 BTB.4: 2 residues within 4Å: Chain A: E.337, T.347 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.337, A:E.337, A:T.347, A:T.347 Salt bridges: A:E.337 BTB.5: 2 residues within 4Å: Chain A: D.257, E.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.257, A:E.258 Salt bridges: A:E.258 BTB.14: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.281, B:E.281 Salt bridges: B:E.281 BTB.15: 2 residues within 4Å: Chain B: D.257, E.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.257 Salt bridges: B:E.258 BTB.18: 6 residues within 4Å: Chain B: W.282, A.285, L.286, D.338, C.342 Ligands: GD.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.282 Salt bridges: B:D.338

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: E.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.127 GOL.7: 1 residues within 4Å: Chain A: Q.217 No protein-ligand interaction detected (PLIP) GOL.11: 2 residues within 4Å: Chain A: D.344, L.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.344

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

CL.8: 3 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, N.326 Ligand excluded by PLIP

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

GD.9: 1 residues within 4Å: Ligands: BTB.3 No protein-ligand interaction detected (PLIP) GD.17: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.11 GD.19: 1 residues within 4Å: Ligands: BTB.18 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain A: C.54, C.59 Chain B: C.54, C.59, G.61 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weerawarna, P.M. et al., Discovery of Tetrahydrobiopterin Displacing Potent Neuronal Nitric Oxide Synthase Inhibitor with Unprecedented Binding Mode: Synthesis, Biochemical Evaluation, and Structural Characterization. To be published

Release Date

2025-06-11

Peptides

Nitric oxide synthase, endothelial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase, endothelial

Related Entries With Identical Sequence