SMTL ID : 7tsg.2 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain in complex with 6-(3-(dimethylamino)propyl)-4-methylpyridin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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, KL0.3 14 PLIP interactions: 14 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:E.321, A:F.433, A:F.433 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.11: 20 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, KL0.13 16 PLIP interactions: 16 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:F.313, B:W.316, B:E.321, B:V.378, B:F.433, B:F.433 Hydrogen bonds: B:Y.435 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 8 PLIP interactions: 7 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 pi-Cation interactions: A:W.407 Hydrophobic interactions: B:E.423 H4B.12: 12 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, GOL.16 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:S.62, B:W.407 pi-Stacking: B:W.407, B:W.407 pi-Cation interactions: B:W.407 Hydrophobic interactions: A:E.423

2 x KL0: 6-[3-(dimethylamino)propyl]-4-methylpyridin-2-amine(Non-covalent)

KL0.3: 12 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 Ligands: HEM.1, CL.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.294, A:F.313 Hydrogen bonds: A:M.318, A:E.321 KL0.13: 12 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 Ligands: HEM.11, CL.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.294, B:F.313 Hydrogen bonds: B:M.318, B:E.321

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

BTB.4: 4 residues within 4Å: Chain A: W.282, V.341, C.342, D.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.344 Water bridges: A:W.282 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, A:T.347 Salt bridges: A:E.337 BTB.6: 1 residues within 4Å: Chain A: E.258 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.281, B:E.281 Water bridges: B:T.279, B:T.279, B:T.279 Salt bridges: B:E.281 BTB.15: 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

3 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: Q.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217, A:Q.217 GOL.16: 6 residues within 4Å: Chain A: W.34 Chain B: V.64, R.325, H.331, W.407 Ligands: H4B.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.325, B:R.325, B:H.331

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

CL.9: 4 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligands: KL0.3 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, N.326 Ligands: KL0.13 Ligand excluded by PLIP

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

1 x GD: GADOLINIUM ATOM(Non-covalent)

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.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasu, D. et al., 2-Aminopyridines with a shortened amino sidechain as potent, selective, and highly permeable human neuronal nitric oxide synthase inhibitors. Bioorg.Med.Chem. (2022)

Release Date

2022-07-13

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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