SMTL ID : 9q4x.1 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain bound with 6-((5-(2-(dimethylamino)ethyl)-2,3-difluorophenoxy)methyl)-4-methylpyridin-2-amine

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: 18 residues within 4Å: Chain A: W.138, A.141, 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.2, 01.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: 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:E.321, A:F.433, A:F.433, A:F.433 Hydrogen bonds: A:R.143, A:Y.435 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.12: 17 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, V.145, 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 17 PLIP interactions: 17 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:W.316, B:E.321, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:R.143, 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: 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, 01.3 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, A:W.407 Hydrophobic interactions: B:E.423 H4B.13: 12 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, 01.14, GOL.17 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 01: 6-({5-[2-(dimethylamino)ethyl]-2,3-difluorophenoxy}methyl)-4-methylpyridin-2-amine

01.3: 12 residues within 4Å: Chain A: P.294, V.296, M.299, F.313, S.314, G.315, W.316, Y.317, E.321, Y.435 Ligands: HEM.1, H4B.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.294, A:V.296, A:F.313 Hydrogen bonds: A:M.318, A:E.321 01.14: 15 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, N.326, Y.435 Ligands: HEM.12, H4B.13, GOL.17 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: GD.9 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.337, A:T.347, A:T.347 Salt bridges: A:E.337 BTB.15: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.19 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.281, B:E.281 Water bridges: B:T.279, B:T.279 Salt bridges: B:E.281 BTB.16: 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: E.127 No protein-ligand interaction detected (PLIP) GOL.7: 1 residues within 4Å: Chain A: E.258 No protein-ligand interaction detected (PLIP) GOL.17: 7 residues within 4Å: Chain A: W.34, H.421 Chain B: R.325, H.331, W.407 Ligands: H4B.13, 01.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.421, B:R.325

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.18: 5 residues within 4Å: Chain B: Q.207, R.210, Y.291, 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.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.5

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

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.11: 1 residues within 4Å: Chain A: Q.217 No protein-ligand interaction detected (PLIP) CA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ansari, A. et al., Highly potent, selective, and membrane permeable ether linked 2-aminopyridine-based human neuronal nitric oxide synthase inhibitors. To Be Published

Release Date

2025-09-10

Peptides

Nitric oxide synthase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase 3

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