SMTL ID : 9cw6.2 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain bound with 6-(3-chloro-5-((dimethylamino)methyl)phenyl)-4-methylpyridin-2-amine dihydrochloride

Coordinates

PDB Format Compare

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, P.142, R.143, C.144, 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.2, 01.3 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:W.138, A:A.141, A:R.143, A:L.153, 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 Hydrogen bonds: A:R.143, A:Y.435 Salt bridges: A:R.143 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.12: 19 residues within 4Å: Chain B: W.138, A.141, P.142, R.143, C.144, V.145, G.146, S.186, F.313, S.314, G.315, W.316, M.318, E.321, W.407, F.433, Y.435 Ligands: H4B.13, 01.14 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:R.143, B:F.313, B:F.313, B:F.313, B:F.313, B:W.316, B:W.407, B:W.407, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:R.143, B:Y.435 Salt bridges: 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: 10 residues within 4Å: Chain A: S.62, V.64, R.325, A.406, W.407 Chain B: W.405, F.420, H.421, 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.13: 10 residues within 4Å: Chain A: W.405, F.420, Q.422, E.423 Chain B: S.62, V.64, R.325, A.406, W.407 Ligands: HEM.12 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:S.62, B:L.63 pi-Stacking: B:W.407, B:W.407 Hydrophobic interactions: A:E.423

2 x 01: (6P)-6-{3-chloro-5-[(dimethylamino)methyl]phenyl}-4-methylpyridin-2-amine

01.3: 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, N.326, Y.435 Ligands: HEM.1, CL.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.294, A:V.296, A:F.313 Hydrogen bonds: A:M.318, A:E.321 Halogen bonds: A:Y.435 01.14: 13 residues within 4Å: Chain B: Q.207, P.294, V.296, M.299, F.313, S.314, G.315, W.316, Y.317, M.318, E.321 Ligands: HEM.12, CL.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.294, B:V.296, B:F.313 Hydrogen bonds: B:M.318, B:E.321

4 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: GD3.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.344 BTB.5: 2 residues within 4Å: Chain A: D.257, E.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.257 Salt bridges: A:E.258 BTB.15: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD3.19 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.257 Salt bridges: B:E.258

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: E.127 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.157, A:D.157 GOL.7: 1 residues within 4Å: Chain A: V.36 No protein-ligand interaction detected (PLIP) GOL.8: 1 residues within 4Å: Chain A: G.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.197 GOL.17: 2 residues within 4Å: Chain B: T.43, K.396 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.43, B:K.396

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

CL.9: 4 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligands: 01.3 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, N.326 Ligands: 01.14 Ligand excluded by PLIP

2 x GD3: GADOLINIUM ION(Non-covalent)

GD3.10: 2 residues within 4Å: Chain A: D.344 Ligands: BTB.4 No protein-ligand interaction detected (PLIP) GD3.19: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.3

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 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., 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
C

B
D

Nitric oxide synthase, endothelial

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