SMTL ID : 7tsi.1 (1 other biounit)

Structure of human endothelial nitric oxide synthase heme domain in complex with 4-methyl-6-(3-((methylamino)methyl)phenyl)pyridin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, 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, KMI.3 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:W.138, A:A.141, A:V.145, A:F.313, A:F.313, A:F.313, A:F.313, A:W.316, 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:Y.435 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.13: 21 residues within 4Å: Chain B: W.138, A.141, 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.14, KMI.15 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:L.153, 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, B:F.433 Hydrogen bonds: B:R.143 Water bridges: B:R.325, B:R.325, 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.34, W.405, F.420, H.421, Q.422, 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.14: 13 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.13, GOL.18 8 PLIP interactions: 7 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 pi-Cation interactions: B:W.407 Hydrophobic interactions: A:E.423

2 x KMI: 4-methyl-6-{3-[(methylamino)methyl]phenyl}pyridin-2-amine(Non-covalent)

KMI.3: 13 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 Ligands: HEM.1, CL.10 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, A:E.321 KMI.15: 13 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, N.326 Ligands: HEM.13, CL.20 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.294, B:V.296, B:F.313 Hydrogen bonds: B:M.318, B:E.321, B:E.321, B:E.321

5 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.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.344 BTB.5: 3 residues within 4Å: Chain A: E.337, T.347, R.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.337, A:T.347 Salt bridges: A:E.337 BTB.6: 1 residues within 4Å: Chain A: E.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.258 Salt bridges: A:E.258 BTB.16: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.21 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.281 BTB.17: 2 residues within 4Å: Chain B: D.257, E.258 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.258

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: E.127 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.157 GOL.8: 1 residues within 4Å: Chain A: Q.217 No protein-ligand interaction detected (PLIP) GOL.9: 5 residues within 4Å: Chain A: V.364, H.368, Q.371 Chain B: S.351, S.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.368, A:Q.371 GOL.18: 7 residues within 4Å: Chain A: W.34 Chain B: V.64, R.325, D.329, H.331, W.407 Ligands: H4B.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.325, B:D.329, B:D.329 Water bridges: B:R.325, B:R.325 GOL.19: 2 residues within 4Å: Chain B: E.337, D.338 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.337, B:E.337, B:D.338 Water bridges: B:D.338

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

CL.10: 6 residues within 4Å: Chain A: Q.207, R.210, Y.291, Y.317, N.326 Ligands: KMI.3 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: Q.207, Y.291, Y.317, N.326 Ligands: KMI.15 Ligand excluded by PLIP

2 x GD: GADOLINIUM ATOM(Non-covalent)

GD.11: 2 residues within 4Å: Chain A: D.344 Ligands: BTB.4 No protein-ligand interaction detected (PLIP) GD.21: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.8

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain A: C.54, C.59 Chain B: C.54, C.59, G.61 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., 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
A

B
B

Nitric oxide synthase, endothelial

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