SMTL ID : 8fgu.1 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(difluoromethyl)-6-(5-(2-(dimethylamino)ethyl)-2,3-difluorophenethyl)pyridin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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, G.146, S.186, M.299, F.313, S.314, W.316, M.318, E.321, W.407, F.433, Y.435 Ligands: H4B.2, XVA.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:W.138, A:A.141, A:F.313, A:F.313, A:F.313, A:F.313, A:W.316, A:W.316, A:E.321, A:W.407, A:F.433, A:F.433, A:F.433 Hydrogen bonds: A:Y.435 Water bridges: A:R.325 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.11: 19 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, V.145, G.146, L.153, S.186, F.313, S.314, G.315, W.316, M.318, E.321, W.407, F.433, Y.435 Ligands: H4B.12, XVA.13 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:L.153, B:F.313, 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:R.143 Water bridges: B:E.321 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, XVA.3 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 pi-Cation interactions: A:W.407 Hydrophobic interactions: B:E.423 H4B.12: 13 residues within 4Å: Chain A: W.34, W.405, F.420, H.421, Q.422, E.423 Chain B: S.62, V.64, R.325, A.406, W.407 Ligands: HEM.11, XVA.13 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.325, B:R.325, B:A.406, B:W.407 Water bridges: B:G.61, B:S.62 pi-Stacking: B:W.407, B:W.407 pi-Cation interactions: B:W.407 Hydrophobic interactions: A:E.423

2 x XVA: 4-(difluoromethyl)-6-(2-{5-[2-(dimethylamino)ethyl]-2,3-difluorophenyl}ethyl)pyridin-2-amine(Non-covalent)

XVA.3: 14 residues within 4Å: Chain A: Q.207, P.294, V.296, F.313, S.314, G.315, W.316, Y.317, M.318, E.321, R.325 Ligands: HEM.1, H4B.2, CL.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.294 Hydrogen bonds: A:W.316, A:M.318 Halogen bonds: A:F.313 XVA.13: 13 residues within 4Å: Chain B: P.294, V.296, F.313, S.314, G.315, W.316, Y.317, M.318, E.321, R.325, Y.435 Ligands: HEM.11, H4B.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.294 Hydrogen bonds: B:M.318, B:E.321

6 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.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.344 Salt bridges: A:D.344 BTB.5: 3 residues within 4Å: Chain A: E.337, T.347, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.337, A:E.337, A:T.347 Water bridges: A:T.347 Salt bridges: A:E.337 BTB.6: 2 residues within 4Å: Chain A: E.258, P.259 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.258 BTB.14: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.18 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.19: 1 residues within 4Å: Chain B: D.344 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.344

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: E.127 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.127 GOL.16: 1 residues within 4Å: Chain B: E.337 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.337

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

CL.8: 4 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligands: XVA.3 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: Q.207, Y.317, N.326 Ligand excluded by PLIP

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

GD.9: 1 residues within 4Å: Ligands: BTB.4 No protein-ligand interaction detected (PLIP) GD.18: 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

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasu, D. et al., Potent, Selective, and Membrane Permeable 2-Amino-4-Substituted Pyridine-Based Neuronal Nitric Oxide Synthase Inhibitors. J.Med.Chem. (2023)

Release Date

2023-10-11

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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