SMTL ID : 4imx.1

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 3,5-bis(2-(6-amino-4-methylpyridin-2-yl)ethyl)benzonitrile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: W.140, A.143, R.145, C.146, V.147, G.148, S.188, M.301, F.315, S.316, G.317, W.318, M.320, E.323, W.409, F.435, Y.437 Ligands: H4B.2, 1EV.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:W.140, A:W.140, A:W.140, A:A.143, A:R.145, A:F.315, A:F.315, A:F.315, A:F.315, A:W.318, A:W.318, A:E.323, A:W.409, A:F.435, A:F.435, A:F.435 Hydrogen bonds: A:Y.437 Water bridges: A:E.323, A:R.327, A:R.327 pi-Stacking: A:W.140 Metal complexes: A:C.146 HEM.9: 21 residues within 4Å: Chain B: W.140, A.143, R.145, C.146, V.147, G.148, L.155, S.188, M.301, F.315, S.316, G.317, W.318, M.320, E.323, V.380, W.409, F.435, Y.437 Ligands: H4B.10, 1EV.11 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.140, B:W.140, B:A.143, B:R.145, B:L.155, B:F.315, B:F.315, B:F.315, B:F.315, B:W.318, B:E.323, B:V.380, B:W.409, B:F.435, B:F.435, B:F.435 pi-Stacking: B:W.140 Metal complexes: B:C.146

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 12 residues within 4Å: Chain A: S.64, V.66, R.327, A.408, W.409 Chain B: W.407, F.422, H.423, Q.424, E.425 Ligands: HEM.1, GOL.6 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.327, A:R.327, A:A.408, A:W.409 Water bridges: A:S.64, A:W.409 pi-Stacking: A:W.409, A:W.409 pi-Cation interactions: A:W.409 Hydrophobic interactions: B:E.425 H4B.10: 12 residues within 4Å: Chain A: W.407, F.422, H.423, Q.424, E.425 Chain B: S.64, V.66, R.327, A.408, W.409 Ligands: HEM.9, GOL.14 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.327, B:R.327, B:A.408, B:W.409 pi-Stacking: B:W.409, B:W.409 pi-Cation interactions: B:W.409 Hydrophobic interactions: A:E.425

2 x 1EV: 3,5-bis[2-(6-amino-4-methylpyridin-2-yl)ethyl]benzonitrile(Non-covalent)

1EV.3: 17 residues within 4Å: Chain A: L.67, S.208, Q.209, R.212, P.296, V.298, F.315, S.316, G.317, W.318, Y.319, E.323, W.409, Y.437 Ligands: HEM.1, ACT.5, GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.296, A:F.315, A:W.409 Hydrogen bonds: A:Q.209, A:M.320, A:E.323 1EV.11: 18 residues within 4Å: Chain A: W.36 Chain B: S.208, Q.209, R.212, P.296, V.298, F.315, S.316, G.317, W.318, Y.319, M.320, E.323, W.409, Y.437 Ligands: HEM.9, ACT.13, GOL.14 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.296, B:V.298, B:F.315, B:W.409, A:W.36 Hydrogen bonds: B:Q.209, B:M.320, B:E.323 Water bridges: B:N.300

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

ACT.4: 4 residues within 4Å: Chain A: G.148, W.318, V.380, S.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.388, A:S.388 ACT.5: 5 residues within 4Å: Chain A: Q.209, R.212, N.328, R.334 Ligands: 1EV.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.209, A:N.328 Salt bridges: A:R.212, A:R.334 ACT.12: 4 residues within 4Å: Chain B: G.148, W.318, V.380, S.388 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.318, B:S.388 ACT.13: 5 residues within 4Å: Chain B: Q.209, R.212, N.328, R.334 Ligands: 1EV.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.209, B:N.328, B:N.328 Salt bridges: B:R.212, B:R.334

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: V.66, R.327, H.333, W.409 Chain B: W.36 Ligands: H4B.2, 1EV.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.327, A:R.327, A:H.333 GOL.14: 7 residues within 4Å: Chain A: W.36 Chain B: V.66, R.327, H.333, W.409 Ligands: H4B.10, 1EV.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.327, B:R.327, B:H.333 Water bridges: B:D.331, A:H.423

2 x CAD: CACODYLIC ACID(Non-covalent)

CAD.7: 3 residues within 4Å: Chain A: W.284, L.288, C.344 No protein-ligand interaction detected (PLIP) CAD.15: 2 residues within 4Å: Chain B: W.284, C.344 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: C.56, C.61 Chain B: C.56, C.61, G.63 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.56, A:C.61, B:C.56, B:C.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., Structure-guided design of selective inhibitors of neuronal nitric oxide synthase. J.Med.Chem. (2013)

Release Date

2013-04-24

Peptides

subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

subunit A