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

Structure of human endothelial nitric oxide synthase heme domain bound with 6-(5-((4,4-difluoropiperidin-1-yl)methyl)-2,3-difluorophenyl)-4-methylpyridin-2-amine dihydrochloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: W.138, A.141, P.142, R.143, C.144, V.145, G.146, L.153, 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: H4B.2, 01.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:W.138, A:A.141, A:R.143, 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:R.143, A:E.321, A:E.321 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.14: 20 residues within 4Å: Chain B: W.138, A.141, P.142, R.143, C.144, V.145, G.146, L.153, S.186, M.299, F.313, S.314, G.315, W.316, M.318, E.321, W.407, F.433 Ligands: H4B.15, 01.16 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:R.143, 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 pi-Stacking: B:W.138 Metal complexes: B:C.144

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

H4B.2: 13 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, 01.3, GOL.9 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.325, A:R.325, A:A.406, A:W.407 Water bridges: A:S.62, A:L.63 pi-Stacking: A:W.407, A:W.407 pi-Cation interactions: A:W.407 Hydrophobic interactions: B:E.423 H4B.15: 14 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.14, 01.16, GOL.20 9 PLIP interactions: 8 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:L.63, B:W.407 pi-Stacking: B:W.407, B:W.407 Hydrophobic interactions: A:E.423

2 x 01: (6M)-6-{5-[(4,4-difluoropiperidin-1-yl)methyl]-2,3-difluorophenyl}-4-methylpyridin-2-amine

01.3: 17 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, N.326, R.332 Ligands: HEM.1, H4B.2, GOL.9, CL.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.294, A:F.313, A:R.325 Hydrogen bonds: A:M.318, A:E.321 01.16: 16 residues within 4Å: Chain B: Q.207, P.294, V.296, F.313, S.314, G.315, W.316, Y.317, M.318, E.321, R.325, N.326, R.332 Ligands: HEM.14, H4B.15, CL.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.294, B:F.313, B:R.325 Hydrogen bonds: B:M.318, B:E.321 Water bridges: B:R.332

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: GD3.11 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.337, A:T.347 Water bridges: A:T.347, A:W.354 BTB.6: 3 residues within 4Å: Chain A: D.257, E.258, P.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.257, A:E.258 Salt bridges: A:E.258 BTB.17: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD3.22 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.279 Salt bridges: B:E.281 BTB.18: 2 residues within 4Å: Chain B: D.257, E.258 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.258 Salt bridges: B:E.258 BTB.23: 6 residues within 4Å: Chain B: W.282, A.285, L.286, D.338, C.342 Ligands: GD3.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.282

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: E.127 No protein-ligand interaction detected (PLIP) GOL.8: 1 residues within 4Å: Chain A: G.197 No protein-ligand interaction detected (PLIP) GOL.9: 6 residues within 4Å: Chain A: V.64, R.325, H.331 Chain B: W.34 Ligands: H4B.2, 01.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.325, A:H.331 GOL.13: 2 residues within 4Å: Chain A: D.344, L.345 No protein-ligand interaction detected (PLIP) GOL.19: 1 residues within 4Å: Chain B: E.337 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.337 GOL.20: 6 residues within 4Å: Chain A: W.34 Chain B: V.64, R.325, H.331, W.407 Ligands: H4B.15 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.325, B:H.331 Water bridges: B:D.329, A:H.421

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

CL.10: 5 residues within 4Å: Chain A: Q.207, Y.291, Y.317, N.326 Ligands: 01.3 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, N.326 Ligands: 01.16 Ligand excluded by PLIP

3 x GD3: GADOLINIUM ION(Non-functional Binders)(Non-covalent)

GD3.11: 1 residues within 4Å: Ligands: BTB.4 No protein-ligand interaction detected (PLIP) GD3.22: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.12 GD3.24: 1 residues within 4Å: Ligands: BTB.23 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasu, D. et al., Truncated pyridinylbenzylamines: Potent, selective, and highly membrane permeable inhibitors of human neuronal nitric oxide synthase. Bioorg.Med.Chem. (2025)

Release Date

2025-04-30

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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