SMTL ID : 7m56.1

Structure of human endothelial nitric oxide synthase heme domain in complex with 7-((3-(3-aminophenethyl)phenoxy)methyl)quinolin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 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, 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, V5G.3, ACT.6 17 PLIP interactions: 17 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:W.316, A:E.321, A:F.433, A:F.433, A:F.433 Water bridges: A:R.325 Salt bridges: A:R.143 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.11: 21 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, V.378, W.407, F.433, Y.435 Ligands: H4B.12, V5G.13, ACT.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:L.153, B:F.313, B:F.313, B:F.313, B:W.316, B:E.321, B:V.378, B:F.433, B:F.433, B:F.433 Water bridges: B:R.325, B:R.325 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: 11 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 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:E.423 Hydrogen bonds: A:R.325, A:R.325, A:A.406, A:W.407 pi-Stacking: A:W.407, A:W.407 H4B.12: 11 residues within 4Å: Chain A: 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 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:E.423 Water bridges: A:H.421 Hydrogen bonds: B:R.325, B:R.325, B:A.406, B:W.407 pi-Stacking: B:W.407, B:W.407

3 x V5G: 7-({3-[2-(6-aminopyridin-2-yl)ethyl]phenoxy}methyl)quinolin-2-amine(Non-covalent)

V5G.3: 11 residues within 4Å: Chain A: P.294, V.296, N.298, M.299, W.316, Y.317, M.318, E.321, Y.435, Q.436 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.296, A:Y.435 Hydrogen bonds: A:M.318, A:E.321, A:Q.436 Water bridges: A:N.298, A:Q.436 V5G.4: 6 residues within 4Å: Chain A: W.282, V.341, C.342, D.344, R.348 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.341, A:V.341 Hydrogen bonds: A:D.344 V5G.13: 12 residues within 4Å: Chain B: P.294, V.296, N.298, M.299, F.313, W.316, Y.317, M.318, E.321, Y.435, Q.436 Ligands: HEM.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.294, B:P.294, B:V.296, B:F.313, B:Y.435 Hydrogen bonds: B:M.318, B:E.321, B:Q.436 Water bridges: B:Q.207, B:N.298, B:Q.436 pi-Stacking: B:F.65

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 2 residues within 4Å: Chain A: D.344 Ligands: V5G.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.344 ACT.6: 7 residues within 4Å: Chain A: G.146, I.148, Q.149, W.316, V.378, S.386 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.149 Hydrogen bonds: A:W.316, A:S.386 ACT.14: 5 residues within 4Å: Chain B: G.146, W.316, V.378, S.386 Ligands: HEM.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.316, B:S.386 Water bridges: B:Q.149

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

BTB.7: 2 residues within 4Å: Chain A: E.337, T.347 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.347 Water bridges: A:E.337, A:E.337 Salt bridges: A:E.337 BTB.15: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.281, B:E.281 Water bridges: B:T.279, B:T.279, B:T.279, B:E.281 Salt bridges: B:E.281

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 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 GOL: GLYCEROL(Non-functional Binders)

GOL.9: 1 residues within 4Å: Chain A: E.258 No protein-ligand interaction detected (PLIP) GOL.10: 2 residues within 4Å: Chain A: G.199, D.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.199, A:D.257

1 x GD: GADOLINIUM ATOM(Non-covalent)

GD.16: 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.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, M.C. et al., Inhibition of bacterial nitric oxide synthase as an antimicrobial tool in fighting some antibiotic-resistant pathogens. To be published

Release Date

2022-03-30

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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