Fluorine in PDB 5dig: Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol, PDB code: 5dig was solved by J.C.Nwachukwu, S.Srinivasan, Y.Zheng, S.Wang, J.Min, C.Dong, Z.Liao, V.Cavett, J.Nowak, R.Houtman, K.E.Carlson, J.S.Josan, O.Elemento, J.A.Katzenellenbogen, H.B.Zhou, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.09 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.261, 84.179, 58.905, 90.00, 108.93, 90.00
R / Rfree (%)	18.6 / 21.2

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol (pdb code 5dig). 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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol, PDB code: 5dig:
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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol


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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:30.8 occ:1.00 F01 A:5CE601 0.0 30.8 1.0 C17 A:5CE601 1.3 29.6 1.0 F03 A:5CE601 2.1 28.9 1.0 F02 A:5CE601 2.1 29.8 1.0 C04 A:5CE601 2.4 28.6 1.0 C03 A:5CE601 2.7 27.7 1.0 CD2 A:LEU391 3.2 28.6 1.0 CG A:MET388 3.3 23.6 1.0 CA A:MET388 3.3 26.3 1.0 O A:LEU387 3.6 26.2 1.0 CB A:LEU391 3.7 26.5 1.0 C05 A:5CE601 3.7 27.5 1.0 N A:MET388 3.7 27.4 1.0 CB A:MET388 3.8 24.9 1.0 C A:LEU387 3.8 26.3 1.0 C02 A:5CE601 4.0 27.3 1.0 CG A:LEU391 4.1 28.4 1.0 CD2 A:LEU428 4.1 21.7 1.0 CD1 A:LEU428 4.2 21.9 1.0 C07 A:5CE601 4.4 26.6 1.0 C A:MET388 4.4 27.4 1.0 O A:MET388 4.5 27.3 1.0 CB A:LEU387 4.6 26.2 1.0 CE1 A:PHE404 4.7 25.3 1.0 C06 A:5CE601 4.7 26.4 1.0 O02 A:5CE601 4.8 26.6 1.0 CE A:MET388 4.8 18.5 1.0 CG A:LEU428 4.8 23.5 1.0 SD A:MET388 4.8 24.5 1.0 C01 A:5CE601 4.9 26.8 1.0 CA A:LEU387 4.9 26.4 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol


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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:29.8 occ:1.00 F02 A:5CE601 0.0 29.8 1.0 C17 A:5CE601 1.3 29.6 1.0 F03 A:5CE601 2.1 28.9 1.0 F01 A:5CE601 2.1 30.8 1.0 C04 A:5CE601 2.3 28.6 1.0 C05 A:5CE601 3.0 27.5 1.0 C07 A:5CE601 3.1 26.6 1.0 CG A:MET388 3.2 23.6 1.0 C03 A:5CE601 3.3 27.7 1.0 CD1 A:LEU384 3.4 25.6 1.0 CE A:MET388 3.6 18.5 1.0 C08 A:5CE601 4.0 27.1 1.0 SD A:MET388 4.2 24.5 1.0 C06 A:5CE601 4.2 26.4 1.0 C12 A:5CE601 4.3 24.3 1.0 CB A:MET388 4.3 24.9 1.0 C13 A:5CE601 4.4 27.9 1.0 CG A:LEU384 4.4 26.2 1.0 CA A:MET388 4.4 26.3 1.0 N A:MET388 4.4 27.4 1.0 O A:LEU384 4.5 26.9 1.0 C02 A:5CE601 4.5 27.3 1.0 CB A:LEU387 4.5 26.2 1.0 C A:LEU387 4.7 26.3 1.0 C09 A:5CE601 4.8 28.1 1.0 CD1 A:LEU428 4.8 21.9 1.0 C01 A:5CE601 4.9 26.8 1.0 C11 A:5CE601 4.9 25.5 1.0 O A:LEU387 5.0 26.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol


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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:28.9 occ:1.00 F03 A:5CE601 0.0 28.9 1.0 C17 A:5CE601 1.3 29.6 1.0 F01 A:5CE601 2.1 30.8 1.0 F02 A:5CE601 2.1 29.8 1.0 C04 A:5CE601 2.4 28.6 1.0 C05 A:5CE601 3.0 27.5 1.0 C07 A:5CE601 3.1 26.6 1.0 CD1 A:LEU428 3.4 21.9 1.0 C03 A:5CE601 3.4 27.7 1.0 C12 A:5CE601 3.5 24.3 1.0 CD2 A:LEU391 3.6 28.6 1.0 CE1 A:PHE404 3.8 25.3 1.0 CZ A:PHE404 4.1 24.6 1.0 C11 A:5CE601 4.2 25.5 1.0 C06 A:5CE601 4.3 26.4 1.0 CG A:MET388 4.4 23.6 1.0 CD2 A:LEU428 4.4 21.7 1.0 C08 A:5CE601 4.5 27.1 1.0 CG A:LEU428 4.5 23.5 1.0 C02 A:5CE601 4.6 27.3 1.0 CE A:MET388 4.7 18.5 1.0 CD1 A:PHE404 4.9 27.1 1.0 CG A:LEU391 4.9 28.4 1.0 C01 A:5CE601 4.9 26.8 1.0 C13 A:5CE601 4.9 27.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol


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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:31.4 occ:1.00 F01 B:5CE601 0.0 31.4 1.0 C17 B:5CE601 1.3 32.1 1.0 F03 B:5CE601 2.1 31.6 1.0 F02 B:5CE601 2.1 32.0 1.0 C04 B:5CE601 2.4 32.4 1.0 C03 B:5CE601 2.7 32.2 1.0 CD2 B:LEU391 3.2 33.5 1.0 CA B:MET388 3.3 27.7 1.0 CG B:MET388 3.3 27.3 1.0 CB B:LEU391 3.7 30.6 1.0 C05 B:5CE601 3.7 34.0 1.0 O B:LEU387 3.7 32.4 1.0 N B:MET388 3.8 29.1 1.0 CB B:MET388 3.8 26.4 1.0 C B:LEU387 3.9 30.9 1.0 C02 B:5CE601 4.0 33.2 1.0 CG B:LEU391 4.0 33.5 1.0 CD2 B:LEU428 4.1 26.6 1.0 CD1 B:LEU428 4.2 29.3 1.0 C B:MET388 4.4 26.9 1.0 C07 B:5CE601 4.4 35.6 1.0 O B:MET388 4.5 26.5 1.0 C06 B:5CE601 4.7 34.3 1.0 CB B:LEU387 4.7 30.3 1.0 O02 B:5CE601 4.7 32.6 1.0 CE1 B:PHE404 4.8 34.3 1.0 CG B:LEU428 4.8 28.7 1.0 C01 B:5CE601 4.8 33.7 1.0 CE B:MET388 4.9 25.5 1.0 SD B:MET388 4.9 32.0 1.0 CA B:LEU387 5.0 29.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol


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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:32.0 occ:1.00 F02 B:5CE601 0.0 32.0 1.0 C17 B:5CE601 1.3 32.1 1.0 F03 B:5CE601 2.1 31.6 1.0 F01 B:5CE601 2.1 31.4 1.0 C04 B:5CE601 2.3 32.4 1.0 C05 B:5CE601 3.0 34.0 1.0 CG B:MET388 3.2 27.3 1.0 C07 B:5CE601 3.2 35.6 1.0 C03 B:5CE601 3.3 32.2 1.0 CD1 B:LEU384 3.5 28.1 1.0 CE B:MET388 3.7 25.5 1.0 C08 B:5CE601 4.0 36.2 1.0 C06 B:5CE601 4.3 34.3 1.0 SD B:MET388 4.3 32.0 1.0 CA B:MET388 4.3 27.7 1.0 CB B:MET388 4.3 26.4 1.0 N B:MET388 4.3 29.1 1.0 C12 B:5CE601 4.4 37.0 1.0 C13 B:5CE601 4.4 38.7 1.0 CG B:LEU384 4.5 28.5 1.0 C02 B:5CE601 4.5 33.2 1.0 O B:LEU384 4.5 30.5 1.0 CB B:LEU387 4.5 30.3 1.0 C B:LEU387 4.7 30.9 1.0 C01 B:5CE601 4.9 33.7 1.0 C09 B:5CE601 4.9 38.2 1.0 O B:LEU387 4.9 32.4 1.0 CD1 B:LEU428 5.0 29.3 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol


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 in Complex with A Trifluoromethyl-Substituted A-Cd Ring Estrogen Derivative (1S, 3AR,5S,7AS)-5-[4-Hydroxy-2-(Trifluoromethyl)Phenyl]-7A- Methyloctahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:31.6 occ:1.00 F03 B:5CE601 0.0 31.6 1.0 C17 B:5CE601 1.3 32.1 1.0 F01 B:5CE601 2.1 31.4 1.0 F02 B:5CE601 2.1 32.0 1.0 C04 B:5CE601 2.4 32.4 1.0 C05 B:5CE601 3.0 34.0 1.0 C07 B:5CE601 3.1 35.6 1.0 C03 B:5CE601 3.4 32.2 1.0 CD1 B:LEU428 3.5 29.3 1.0 C12 B:5CE601 3.5 37.0 1.0 CD2 B:LEU391 3.6 33.5 1.0 CE1 B:PHE404 3.9 34.3 1.0 C11 B:5CE601 4.2 38.3 1.0 C06 B:5CE601 4.3 34.3 1.0 CZ B:PHE404 4.4 34.3 1.0 CG B:MET388 4.4 27.3 1.0 C08 B:5CE601 4.4 36.2 1.0 CD2 B:LEU428 4.5 26.6 1.0 C02 B:5CE601 4.6 33.2 1.0 CG B:LEU428 4.6 28.7 1.0 CE B:MET388 4.7 25.5 1.0 C13 B:5CE601 4.9 38.7 1.0 CD1 B:PHE404 4.9 33.8 1.0 C01 B:5CE601 4.9 33.7 1.0 CG B:LEU391 5.0 33.5 1.0

J.C.Nwachukwu, S.Srinivasan, Y.Zheng, S.Wang, J.Min, C.Dong, Z.Liao, J.Nowak, N.J.Wright, R.Houtman, K.E.Carlson, J.S.Josan, O.Elemento, J.A.Katzenellenbogen, H.B.Zhou, K.W.Nettles. Predictive Features of Ligand-Specific Signaling Through the Estrogen Receptor. Mol.Syst.Biol. V. 12 864 2016.
ISSN: ESSN 1744-4292
PubMed: 27107013
DOI: 10.15252/MSB.20156701