SMTL ID : 6cif.1 (1 other biounit)

Structure of the human endothelial nitric oxide synthase heme domain in complex with N-(1-(Piperidin-4-yl)indolin-5-yl)thiophene-2-carboximidamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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, P.142, R.143, C.144, V.145, G.146, S.186, F.313, S.314, G.315, W.316, M.318, E.321, F.433, Y.435 Ligands: H4B.2, F2J.3 18 PLIP interactions: 18 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:F.313, A:W.316, A:E.321, 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.10: 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.11, F2J.12 21 PLIP interactions: 21 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.316, B:E.321, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:R.143, B:Y.435 Water bridges: B:E.321 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 6 PLIP interactions: 5 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 Hydrophobic interactions: B:E.423 H4B.11: 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.10 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 F2J: N-[1-(piperidin-4-yl)-1H-indol-5-yl]thiophene-2-carboximidamide(Non-covalent)

F2J.3: 10 residues within 4Å: Chain A: Q.207, P.294, V.296, F.313, S.314, G.315, W.316, E.321 Ligands: HEM.1, CL.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.294, A:V.296, A:V.296, A:F.313 Hydrogen bonds: A:W.316, A:E.321 F2J.12: 10 residues within 4Å: Chain B: Q.207, P.294, V.296, F.313, S.314, G.315, W.316, E.321 Ligands: HEM.10, CL.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.294, B:V.296, B:V.296, B:F.313 Hydrogen bonds: B:W.316, B:E.321

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

BTB.4: 2 residues within 4Å: Chain A: C.342, D.344 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.344, A:D.344 Salt bridges: A:D.344 BTB.5: 1 residues within 4Å: Chain A: E.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.337 Salt bridges: A:E.337 BTB.13: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.281, B:E.281 Salt bridges: B:E.281 BTB.14: 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 BTB.15: 2 residues within 4Å: Chain B: N.334, D.338 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.334, B:N.334 Salt bridges: B:D.338

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 1 residues within 4Å: Chain A: E.127 No protein-ligand interaction detected (PLIP)

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

CL.8: 4 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligands: F2J.3 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, N.326 Ligands: F2J.12 Ligand excluded by PLIP

2 x GD: GADOLINIUM ATOM(Non-functional Binders)(Non-covalent)

GD.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GD.17: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Structural Basis for Isoform Selective Nitric Oxide Synthase Inhibition by Thiophene-2-carboximidamides. Biochemistry (2018)

Release Date

2018-10-31

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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