Fluorine in PDB 6b0f: Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102

The structure of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102, PDB code: 6b0f was solved by C.A.Kirby, J.Baird, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.84 / 2.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.820, 52.100, 97.020, 90.00, 114.33, 90.00
R / Rfree (%)	22.7 / 29.9

The binding sites of Fluorine atom in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 (pdb code 6b0f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102, PDB code: 6b0f:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:48.4 occ:1.00 F29 A:C6V601 0.0 48.4 1.0 C26 A:C6V601 1.3 47.1 1.0 C25 A:C6V601 2.4 46.6 1.0 C27 A:C6V601 2.4 47.1 1.0 ND1 A:HIS524 3.1 60.3 1.0 CD1 A:ILE424 3.4 56.6 1.0 C28 A:C6V601 3.6 47.6 1.0 CA A:GLY521 3.6 45.6 1.0 CG A:HIS524 3.6 58.2 1.0 C24 A:C6V601 3.7 46.7 1.0 CB A:HIS524 3.7 54.5 1.0 O A:GLY521 3.9 52.5 1.0 CE1 A:HIS524 4.0 59.8 1.0 CG2 A:ILE424 4.0 53.2 1.0 CG A:MET421 4.1 70.6 1.0 C13 A:C6V601 4.2 46.6 1.0 CB A:ILE424 4.2 54.1 1.0 CG1 A:ILE424 4.3 54.5 1.0 C A:GLY521 4.3 51.4 1.0 CG A:LEU525 4.4 56.3 1.0 CD2 A:LEU525 4.4 58.1 1.0 CD2 A:HIS524 4.7 60.1 1.0 N A:GLY521 4.7 45.6 1.0 N A:LEU525 4.8 53.3 1.0 NE2 A:HIS524 4.8 60.0 1.0 C30 A:C6V601 4.9 45.4 1.0

Fluorine binding site 2 out of 6 in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:50.6 occ:1.00 F31 A:C6V601 0.0 50.6 1.0 C30 A:C6V601 1.4 45.4 1.0 F33 A:C6V601 2.2 44.1 1.0 C32 A:C6V601 2.3 38.3 1.0 C24 A:C6V601 2.4 46.7 1.0 CZ A:PHE404 3.1 41.2 1.0 C13 A:C6V601 3.2 46.6 1.0 CE2 A:PHE404 3.2 43.0 1.0 C25 A:C6V601 3.3 46.6 1.0 CE A:MET421 3.5 71.6 1.0 C9 A:C6V601 3.5 44.1 1.0 O12 A:C6V601 3.8 41.3 1.0 C10 A:C6V601 3.8 42.9 1.0 SD A:MET421 4.1 75.2 1.0 CD1 A:LEU346 4.1 39.3 1.0 CE1 A:PHE404 4.3 43.2 1.0 C28 A:C6V601 4.5 47.6 1.0 CD2 A:PHE404 4.5 41.0 1.0 C26 A:C6V601 4.6 47.1 1.0 S8 A:C6V601 4.6 43.9 1.0 CD2 A:LEU346 4.6 39.5 1.0 CG A:MET421 4.6 70.6 1.0 CD2 A:PHE425 4.7 52.8 1.0 C6 A:C6V601 4.9 44.7 1.0 CG A:LEU346 4.9 39.2 1.0

Fluorine binding site 3 out of 6 in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:44.1 occ:1.00 F33 A:C6V601 0.0 44.1 1.0 C30 A:C6V601 1.4 45.4 1.0 F31 A:C6V601 2.2 50.6 1.0 C32 A:C6V601 2.3 38.3 1.0 C24 A:C6V601 2.4 46.7 1.0 C13 A:C6V601 3.0 46.6 1.0 CZ A:PHE404 3.1 41.2 1.0 C9 A:C6V601 3.1 44.1 1.0 CD1 A:LEU428 3.2 49.0 1.0 CE2 A:PHE404 3.2 43.0 1.0 S8 A:C6V601 3.4 43.9 1.0 C25 A:C6V601 3.6 46.6 1.0 C10 A:C6V601 4.0 42.9 1.0 CD2 A:LEU391 4.1 37.4 1.0 C28 A:C6V601 4.4 47.6 1.0 CE1 A:PHE404 4.4 43.2 1.0 CG A:LEU428 4.5 49.0 1.0 C5 A:C6V601 4.5 45.7 1.0 CD2 A:PHE404 4.5 41.0 1.0 CD1 A:LEU402 4.6 46.0 1.0 O12 A:C6V601 4.6 41.3 1.0 C6 A:C6V601 4.8 44.7 1.0 C26 A:C6V601 4.8 47.1 1.0 CD2 A:LEU428 4.8 50.6 1.0 CG2 A:ILE424 4.9 53.2 1.0 CB A:LEU428 5.0 44.9 1.0

Fluorine binding site 4 out of 6 in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:46.6 occ:1.00 F29 B:C6V601 0.0 46.6 1.0 C26 B:C6V601 1.3 44.1 1.0 C25 B:C6V601 2.3 44.1 1.0 C27 B:C6V601 2.4 43.2 1.0 O B:GLY521 3.3 44.2 1.0 CD1 B:ILE424 3.4 62.5 1.0 CB B:HIS524 3.4 48.4 1.0 CA B:GLY521 3.5 38.2 1.0 ND1 B:HIS524 3.6 54.5 1.0 C24 B:C6V601 3.6 45.5 1.0 C28 B:C6V601 3.6 44.4 1.0 CG B:HIS524 3.8 52.5 1.0 C B:GLY521 3.9 44.4 1.0 CG1 B:ILE424 4.1 55.5 1.0 C13 B:C6V601 4.1 47.7 1.0 CG2 B:ILE424 4.2 55.4 1.0 CB B:ILE424 4.4 55.5 1.0 CA B:HIS524 4.6 47.1 1.0 CG B:MET421 4.7 71.2 1.0 CE1 B:HIS524 4.7 53.9 1.0 CG B:LEU525 4.7 36.7 1.0 O B:LYS520 4.7 41.9 1.0 N B:GLY521 4.8 37.6 1.0 C B:HIS524 4.8 50.3 1.0 N B:LEU525 4.8 44.8 1.0 C30 B:C6V601 4.9 44.1 1.0 CD2 B:LEU525 4.9 40.2 1.0 CD2 B:HIS524 5.0 54.5 1.0

Fluorine binding site 5 out of 6 in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:42.2 occ:1.00 F31 B:C6V601 0.0 42.2 1.0 C30 B:C6V601 1.4 44.1 1.0 F33 B:C6V601 2.2 47.5 1.0 C32 B:C6V601 2.3 41.6 1.0 C24 B:C6V601 2.4 45.5 1.0 C13 B:C6V601 3.2 47.7 1.0 C9 B:C6V601 3.3 51.1 1.0 CZ B:PHE404 3.4 44.1 1.0 O12 B:C6V601 3.5 46.9 1.0 C10 B:C6V601 3.5 51.0 1.0 C25 B:C6V601 3.5 44.1 1.0 CD1 B:LEU346 3.5 45.7 1.0 CE1 B:PHE404 3.6 44.8 1.0 S8 B:C6V601 4.4 52.4 1.0 C6 B:C6V601 4.5 53.2 1.0 CE2 B:PHE404 4.5 46.0 1.0 C28 B:C6V601 4.5 44.4 1.0 CD2 B:LEU346 4.5 47.2 1.0 CG B:LEU346 4.6 45.6 1.0 C26 B:C6V601 4.7 44.1 1.0 C14 B:C6V601 4.7 46.6 1.0 SD B:MET421 4.8 76.6 1.0 CD1 B:PHE404 4.8 43.7 1.0 C5 B:C6V601 4.8 54.0 1.0

Fluorine binding site 6 out of 6 in the Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Estrogen Receptor Alpha Ligand Binding Domain in Complex with LSZ102 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:47.5 occ:1.00 F33 B:C6V601 0.0 47.5 1.0 C30 B:C6V601 1.4 44.1 1.0 F31 B:C6V601 2.2 42.2 1.0 C32 B:C6V601 2.3 41.6 1.0 C24 B:C6V601 2.4 45.5 1.0 C13 B:C6V601 3.0 47.7 1.0 C9 B:C6V601 3.2 51.1 1.0 CZ B:PHE404 3.3 44.1 1.0 CD1 B:LEU428 3.4 42.8 1.0 S8 B:C6V601 3.4 52.4 1.0 C25 B:C6V601 3.4 44.1 1.0 CE1 B:PHE404 3.6 44.8 1.0 C10 B:C6V601 4.0 51.0 1.0 C28 B:C6V601 4.3 44.4 1.0 C5 B:C6V601 4.5 54.0 1.0 CD2 B:LEU391 4.5 36.2 1.0 CE2 B:PHE404 4.5 46.0 1.0 C26 B:C6V601 4.6 44.1 1.0 O12 B:C6V601 4.6 46.9 1.0 CD1 B:PHE425 4.6 59.3 1.0 C6 B:C6V601 4.8 53.2 1.0 CG2 B:ILE424 4.8 55.4 1.0 CG B:LEU428 4.9 43.2 1.0 CD1 B:LEU402 4.9 45.4 1.0 CE1 B:PHE425 4.9 61.1 1.0 CD1 B:PHE404 4.9 43.7 1.0 C27 B:C6V601 5.0 43.2 1.0

G.S.Tria, T.Abrams, J.Baird, H.E.Burks, B.Firestone, L.A.Gaither, L.G.Hamann, G.He, C.A.Kirby, S.Kim, F.Lombardo, K.J.Macchi, D.P.Mcdonnell, Y.Mishina, J.D.Norris, J.Nunez, C.Springer, Y.Sun, N.M.Thomsen, C.Wang, J.Wang, B.Yu, C.L.Tiong-Yip, S.Peukert. Discovery of LSZ102, A Potent, Orally Bioavailable Selective Estrogen Receptor Degrader (Serd) For the Treatment of Estrogen Receptor Positive Breast Cancer. J. Med. Chem. V. 61 2837 2018.
ISSN: ISSN 1520-4804
PubMed: 29562737
DOI: 10.1021/ACS.JMEDCHEM.7B01682