Fluorine in PDB 5tlf: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol, PDB code: 5tlf was solved by J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, J.Nowak, D.J.Kojetin, O.Elemento, J.A.Katzenellenbogen, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.28 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.655, 81.567, 58.651, 90.00, 109.96, 90.00
R / Rfree (%)	18.8 / 22.9

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol (pdb code 5tlf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol, PDB code: 5tlf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:51.1 occ:1.00 F14 A:7EF601 0.0 51.1 1.0 C13 A:7EF601 1.3 48.5 1.0 F15 A:7EF601 2.2 49.5 1.0 F16 A:7EF601 2.2 49.8 1.0 C12 A:7EF601 2.3 40.3 1.0 C11 A:7EF601 3.0 34.7 1.0 CD2 A:LEU525 3.2 45.6 1.0 N20 A:7EF601 3.2 37.6 1.0 C17 A:7EF601 3.4 35.5 1.0 ND1 A:HIS524 3.4 66.4 1.0 CE A:MET421 3.4 67.6 1.0 CE A:MET343 3.8 47.9 1.0 CE1 A:HIS524 4.1 70.8 1.0 CG A:LEU525 4.2 44.3 1.0 SD A:MET421 4.2 99.8 1.0 C10 A:7EF601 4.2 33.8 1.0 CG A:HIS524 4.4 64.7 1.0 N21 A:7EF601 4.5 41.3 1.0 SD A:MET343 4.5 62.0 1.0 C18 A:7EF601 4.6 35.1 1.0 CB A:HIS524 4.7 58.5 1.0 O A:GLY521 4.9 39.0 1.0 C19 A:7EF601 4.9 34.4 1.0 CD1 A:LEU525 5.0 42.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:49.5 occ:1.00 F15 A:7EF601 0.0 49.5 1.0 C13 A:7EF601 1.3 48.5 1.0 F14 A:7EF601 2.2 51.1 1.0 F16 A:7EF601 2.2 49.8 1.0 C12 A:7EF601 2.3 40.3 1.0 C17 A:7EF601 2.7 35.5 1.0 CD1 A:ILE424 3.2 45.7 1.0 ND1 A:HIS524 3.4 66.4 1.0 SD A:MET421 3.5 99.8 1.0 CE A:MET421 3.6 67.6 1.0 C11 A:7EF601 3.6 34.7 1.0 CG A:HIS524 3.9 64.7 1.0 CB A:HIS524 4.0 58.5 1.0 C18 A:7EF601 4.1 35.1 1.0 CA A:GLY521 4.2 34.4 1.0 CE1 A:HIS524 4.2 70.8 1.0 CG1 A:ILE424 4.4 42.5 1.0 CG2 A:ILE424 4.4 31.1 1.0 N20 A:7EF601 4.4 37.6 1.0 CB A:ILE424 4.5 35.3 1.0 O A:GLY521 4.6 39.0 1.0 C10 A:7EF601 4.7 33.8 1.0 CD2 A:LEU525 4.8 45.6 1.0 C A:GLY521 4.9 35.3 1.0 C19 A:7EF601 4.9 34.4 1.0 CD2 A:HIS524 4.9 70.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:49.8 occ:1.00 F16 A:7EF601 0.0 49.8 1.0 C13 A:7EF601 1.3 48.5 1.0 F15 A:7EF601 2.2 49.5 1.0 F14 A:7EF601 2.2 51.1 1.0 C12 A:7EF601 2.3 40.3 1.0 C11 A:7EF601 2.9 34.7 1.0 N20 A:7EF601 3.0 37.6 1.0 CA A:GLY521 3.3 34.4 1.0 O A:GLY521 3.3 39.0 1.0 CD2 A:LEU525 3.3 45.6 1.0 C17 A:7EF601 3.4 35.5 1.0 CG A:LEU525 3.5 44.3 1.0 C A:GLY521 3.6 35.3 1.0 CD1 A:LEU525 4.1 42.0 1.0 C10 A:7EF601 4.2 33.8 1.0 N21 A:7EF601 4.3 41.3 1.0 ND1 A:HIS524 4.3 66.4 1.0 CB A:HIS524 4.4 58.5 1.0 CD1 A:ILE424 4.4 45.7 1.0 CE A:MET388 4.6 25.4 1.0 C18 A:7EF601 4.6 35.1 1.0 N A:GLY521 4.7 34.5 1.0 N A:LEU525 4.7 50.0 1.0 N A:MET522 4.7 34.3 1.0 CD2 A:LEU384 4.8 26.6 1.0 CB A:LEU525 4.8 43.3 1.0 CG A:HIS524 4.8 64.7 1.0 C09 A:7EF601 4.9 35.2 1.0 C19 A:7EF601 4.9 34.4 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:55.0 occ:0.81 F14 B:7EF601 0.0 55.0 0.8 C13 B:7EF601 1.3 51.4 0.8 F15 B:7EF601 2.2 47.8 0.8 F16 B:7EF601 2.2 54.5 0.8 C12 B:7EF601 2.3 44.6 0.8 C17 B:7EF601 2.7 42.1 0.8 CD1 B:ILE424 3.3 51.3 1.0 CE B:MET421 3.4 66.3 1.0 ND1 B:HIS524 3.6 59.7 1.0 CG B:MET421 3.6 69.1 1.0 C11 B:7EF601 3.6 40.0 0.8 CG B:HIS524 3.9 59.5 1.0 CB B:HIS524 4.0 55.2 1.0 C18 B:7EF601 4.1 40.5 0.8 SD B:MET421 4.1 0.7 1.0 CE1 B:HIS524 4.3 60.5 1.0 N20 B:7EF601 4.4 39.8 0.8 CG1 B:ILE424 4.4 49.9 1.0 CB B:MET421 4.4 71.0 1.0 CG2 B:ILE424 4.5 41.7 1.0 CA B:GLY521 4.5 34.4 1.0 CB B:ILE424 4.6 45.3 1.0 O B:GLY521 4.7 35.5 1.0 CD1 B:LEU525 4.7 65.7 1.0 C10 B:7EF601 4.7 38.7 0.8 CD2 B:HIS524 4.8 60.4 1.0 C19 B:7EF601 4.9 39.3 0.8

Fluorine binding site 5 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:47.8 occ:0.81 F15 B:7EF601 0.0 47.8 0.8 C13 B:7EF601 1.3 51.4 0.8 F14 B:7EF601 2.2 55.0 0.8 F16 B:7EF601 2.2 54.5 0.8 C12 B:7EF601 2.3 44.6 0.8 C11 B:7EF601 2.9 40.0 0.8 N20 B:7EF601 3.1 39.8 0.8 CD1 B:LEU525 3.2 65.7 1.0 O B:GLY521 3.3 35.5 1.0 CA B:GLY521 3.3 34.4 1.0 C17 B:7EF601 3.4 42.1 0.8 C B:GLY521 3.6 34.8 1.0 CD1 B:ILE424 4.2 51.3 1.0 C10 B:7EF601 4.2 38.7 0.8 CB B:HIS524 4.4 55.2 1.0 N21 B:7EF601 4.4 40.0 0.8 C18 B:7EF601 4.6 40.5 0.8 CG B:LEU525 4.6 62.5 1.0 ND1 B:HIS524 4.6 59.7 1.0 CE B:MET388 4.6 42.0 1.0 N B:GLY521 4.6 35.7 1.0 N B:MET522 4.8 32.8 1.0 N B:LEU525 4.9 54.2 1.0 CG B:HIS524 4.9 59.5 1.0 C19 B:7EF601 4.9 39.3 0.8 CD2 B:LEU384 4.9 33.8 1.0 C09 B:7EF601 5.0 37.9 0.8

Fluorine binding site 6 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the Constrained Way Derivative, 4-(2-(3-Methylbut-2-En- 1-Yl)-7-(Trifluoromethyl)-2H-Indazol-3-Yl)Benzene-1,3-Diol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:54.5 occ:0.81 F16 B:7EF601 0.0 54.5 0.8 C13 B:7EF601 1.3 51.4 0.8 F14 B:7EF601 2.2 55.0 0.8 F15 B:7EF601 2.2 47.8 0.8 C12 B:7EF601 2.3 44.6 0.8 C11 B:7EF601 2.9 40.0 0.8 N20 B:7EF601 3.1 39.8 0.8 CD1 B:LEU525 3.2 65.7 1.0 C17 B:7EF601 3.4 42.1 0.8 CE B:MET421 3.4 66.3 1.0 ND1 B:HIS524 3.7 59.7 1.0 C10 B:7EF601 4.2 38.7 0.8 SD B:MET528 4.3 0.4 1.0 N21 B:7EF601 4.4 40.0 0.8 CE1 B:HIS524 4.5 60.5 1.0 CG B:HIS524 4.6 59.5 1.0 C18 B:7EF601 4.6 40.5 0.8 CB B:HIS524 4.7 55.2 1.0 SD B:MET343 4.7 76.2 1.0 CG B:LEU525 4.7 62.5 1.0 SD B:MET421 4.7 0.7 1.0 O B:GLY521 4.8 35.5 1.0 C25 B:7EF601 4.9 56.0 0.8 C24 B:7EF601 4.9 52.8 0.8 C19 B:7EF601 4.9 39.3 0.8 C09 B:7EF601 5.0 37.9 0.8 CE B:MET528 5.0 47.2 1.0

J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, J.Nowak, N.J.Wright, F.Minutolo, E.S.Rangarajan, T.Izard, X.Q.Yao, B.J.Grant, D.J.Kojetin, O.Elemento, J.A.Katzenellenbogen, K.W.Nettles. Systems Structural Biology Analysis of Ligand Effects on Er Alpha Predicts Cellular Response to Environmental Estrogens and Anti-Hormone Therapies. Cell Chem Biol V. 24 35 2017.
ISSN: ESSN 2451-9456
PubMed: 28042045
DOI: 10.1016/J.CHEMBIOL.2016.11.014