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

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol, PDB code: 5did 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)	46.46 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.942, 82.990, 58.273, 90.00, 109.02, 90.00
R / Rfree (%)	18.4 / 22.8

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol (pdb code 5did). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol, PDB code: 5did:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-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 Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:29.1 occ:1.00 F01 A:5CK601 0.0 29.1 1.0 C13 A:5CK601 1.3 30.9 1.0 C14 A:5CK601 2.3 32.9 1.0 C12 A:5CK601 2.3 27.3 1.0 F02 A:5CK601 2.6 30.7 1.0 C10 A:5CK601 2.8 24.1 1.0 CG A:MET388 3.4 22.9 1.0 C11 A:5CK601 3.5 28.7 1.0 C15 A:5CK601 3.5 33.5 1.0 C05 A:5CK601 3.7 21.6 1.0 CE A:MET388 4.0 22.0 1.0 CD2 A:LEU391 4.0 26.4 1.0 C01 A:5CK601 4.0 21.3 1.0 C16 A:5CK601 4.0 30.5 1.0 CD1 A:LEU384 4.2 21.7 1.0 CE1 A:PHE404 4.3 26.3 1.0 CD1 A:LEU428 4.4 23.4 1.0 CA A:MET388 4.5 24.2 1.0 CB A:MET388 4.5 23.1 1.0 SD A:MET388 4.6 24.0 1.0 O02 A:5CK601 4.6 34.9 1.0 C04 A:5CK601 4.7 22.7 1.0 N A:MET388 4.7 24.3 1.0 C A:LEU387 5.0 23.4 1.0 CB A:LEU387 5.0 22.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-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 Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:30.7 occ:1.00 F02 A:5CK601 0.0 30.7 1.0 C14 A:5CK601 1.3 32.9 1.0 C15 A:5CK601 2.3 33.5 1.0 C13 A:5CK601 2.3 30.9 1.0 F01 A:5CK601 2.6 29.1 1.0 O02 A:5CK601 2.7 34.9 1.0 O A:LEU387 2.8 24.6 1.0 C A:LEU387 3.2 23.4 1.0 CB A:LEU391 3.3 24.1 1.0 CD2 A:LEU391 3.4 26.4 1.0 C16 A:5CK601 3.5 30.5 1.0 N A:MET388 3.5 24.3 1.0 C12 A:5CK601 3.5 27.3 1.0 CA A:MET388 3.6 24.2 1.0 CB A:LEU387 3.7 22.1 1.0 CG A:LEU391 3.9 25.7 1.0 C11 A:5CK601 4.0 28.7 1.0 CA A:LEU387 4.0 22.6 1.0 CG A:MET388 4.2 22.9 1.0 O A:HOH724 4.4 24.2 1.0 CB A:MET388 4.5 23.1 1.0 CA A:LEU391 4.5 25.1 1.0 C A:MET388 4.6 25.3 1.0 CD1 A:LEU391 4.6 27.1 1.0 N A:LEU391 4.6 24.5 1.0 CE1 A:PHE404 4.7 26.3 1.0 C10 A:5CK601 4.8 24.1 1.0 O A:MET388 4.8 26.5 1.0 CG A:LEU387 4.9 24.4 1.0 CD1 A:PHE404 4.9 28.0 1.0 NH2 A:ARG394 5.0 24.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-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 Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:40.3 occ:1.00 F01 B:5CK601 0.0 40.3 1.0 C13 B:5CK601 1.3 36.0 1.0 C14 B:5CK601 2.3 32.4 1.0 C12 B:5CK601 2.3 35.5 1.0 F02 B:5CK601 2.6 33.3 1.0 C10 B:5CK601 2.8 32.5 1.0 CG B:MET388 3.3 25.5 1.0 C11 B:5CK601 3.5 35.8 1.0 C15 B:5CK601 3.5 34.8 1.0 C05 B:5CK601 3.7 31.6 1.0 CE B:MET388 4.0 26.1 1.0 C01 B:5CK601 4.0 32.1 1.0 C16 B:5CK601 4.0 36.5 1.0 CD2 B:LEU391 4.0 29.1 1.0 CD1 B:LEU384 4.1 25.1 1.0 CA B:MET388 4.3 25.1 1.0 CD1 B:LEU428 4.3 31.0 1.0 CB B:MET388 4.4 24.9 1.0 N B:MET388 4.5 26.8 1.0 SD B:MET388 4.5 28.1 1.0 CE1 B:PHE404 4.6 33.9 1.0 O02 B:5CK601 4.7 31.2 1.0 C04 B:5CK601 4.8 34.3 1.0 CB B:LEU387 4.8 26.5 1.0 C B:LEU387 4.8 27.0 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-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 Difluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR,5S, 7AS)-5-(2,3-Difluoro-4-Hydroxyphenyl)-7A-Methyloctahydro-1H-Inden-1- Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:33.3 occ:1.00 F02 B:5CK601 0.0 33.3 1.0 C14 B:5CK601 1.3 32.4 1.0 C15 B:5CK601 2.3 34.8 1.0 C13 B:5CK601 2.3 36.0 1.0 F01 B:5CK601 2.6 40.3 1.0 O02 B:5CK601 2.7 31.2 1.0 O B:LEU387 2.9 27.1 1.0 C B:LEU387 3.0 27.0 1.0 CB B:LEU391 3.2 27.8 1.0 N B:MET388 3.3 26.8 1.0 CA B:MET388 3.5 25.1 1.0 C16 B:5CK601 3.5 36.5 1.0 CB B:LEU387 3.5 26.5 1.0 C12 B:5CK601 3.5 35.5 1.0 CD2 B:LEU391 3.6 29.1 1.0 CA B:LEU387 3.8 26.6 1.0 CG B:LEU391 4.0 29.0 1.0 O B:HOH719 4.0 33.6 1.0 C11 B:5CK601 4.0 35.8 1.0 CG B:MET388 4.2 25.5 1.0 CA B:LEU391 4.4 28.5 1.0 N B:LEU391 4.4 27.9 1.0 CB B:MET388 4.4 24.9 1.0 C B:MET388 4.4 25.1 1.0 O B:MET388 4.7 27.7 1.0 CD1 B:LEU391 4.7 28.0 1.0 CG B:LEU387 4.8 27.5 1.0 C10 B:5CK601 4.8 32.5 1.0 NH2 B:ARG394 4.9 31.9 1.0 CE1 B:PHE404 5.0 33.9 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