Fluorine in PDB 3e7c: Glucocorticoid Receptor Lbd Bound to GSK866

The structure of Glucocorticoid Receptor Lbd Bound to GSK866, PDB code: 3e7c was solved by K.P.Madauss, S.P.Williams, I.Mclay, E.L.Stewart, R.K.Bledsoe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.15
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	126.654, 126.654, 78.991, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 26.6

The structure of Glucocorticoid Receptor Lbd Bound to GSK866 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Glucocorticoid Receptor Lbd Bound to GSK866 (pdb code 3e7c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Glucocorticoid Receptor Lbd Bound to GSK866, PDB code: 3e7c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:58.9 occ:1.00 F1 A:8661 0.0 58.9 1.0 C13 A:8661 1.3 64.4 1.0 C14 A:8661 2.3 49.0 1.0 C12 A:8661 2.3 60.7 1.0 NH1 A:ARG611 2.9 65.0 0.5 CZ A:ARG611 3.3 70.4 0.5 O A:ALA607 3.4 55.1 1.0 CG A:ARG611 3.5 56.3 0.5 C A:ALA607 3.6 58.3 1.0 C15 A:8661 3.6 54.6 1.0 C11 A:8661 3.6 53.7 1.0 CB A:ALA607 3.6 37.2 1.0 NH2 A:ARG611 3.8 71.5 0.5 N A:LEU608 3.9 61.5 1.0 NE A:ARG611 4.0 73.7 0.5 C10 A:8661 4.1 51.0 1.0 CA A:LEU608 4.2 62.9 1.0 CA A:ALA607 4.2 50.1 1.0 CD A:ARG611 4.3 65.7 0.5 CB A:ARG611 4.4 58.5 0.5 O A:HOH787 4.4 71.3 1.0 NE2 A:GLN570 4.7 60.9 1.0 O A:HOH794 4.8 62.3 1.0 O A:HOH814 4.9 85.1 1.0 OE1 A:GLN570 4.9 62.6 1.0

Fluorine binding site 2 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:53.8 occ:1.00 F2 A:8661 0.0 53.8 1.0 C16 A:8661 1.3 52.4 1.0 F3 A:8661 2.2 50.5 1.0 F4 A:8661 2.2 57.9 1.0 C4 A:8661 2.4 50.9 1.0 O1 A:8661 2.6 51.2 1.0 N2 A:8661 2.8 45.4 1.0 C5 A:8661 3.0 53.0 1.0 CD1 A:LEU753 3.6 61.7 1.0 C3 A:8661 3.6 50.6 1.0 O A:LEU563 3.6 66.6 1.0 CA A:GLY567 3.6 49.3 1.0 C6 A:8661 3.7 45.2 1.0 CA A:ASN564 4.2 66.0 1.0 OD1 A:ASN564 4.3 68.4 1.0 C7 A:8661 4.3 42.4 1.0 C8 A:8661 4.3 44.5 1.0 C A:LEU563 4.3 68.6 1.0 C A:GLY567 4.4 58.5 1.0 N A:GLY567 4.4 55.7 1.0 O2 A:8661 4.5 42.0 1.0 CZ3 A:TRP600 4.5 58.3 1.0 O A:ASN564 4.5 64.0 1.0 N A:ASN564 4.5 71.5 1.0 N A:GLY568 4.7 62.9 1.0 C A:ASN564 4.8 63.0 1.0 N1 A:8661 4.8 65.3 1.0 CG A:LEU753 4.8 69.4 1.0

Fluorine binding site 3 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:50.5 occ:1.00 F3 A:8661 0.0 50.5 1.0 C16 A:8661 1.3 52.4 1.0 F2 A:8661 2.2 53.8 1.0 F4 A:8661 2.2 57.9 1.0 C4 A:8661 2.4 50.9 1.0 C5 A:8661 2.7 53.0 1.0 C3 A:8661 3.0 50.6 1.0 N2 A:8661 3.1 45.4 1.0 CE A:MET601 3.3 61.0 1.0 O1 A:8661 3.5 51.2 1.0 CZ3 A:TRP600 3.6 58.3 1.0 C6 A:8661 3.8 45.2 1.0 CH2 A:TRP600 3.8 60.8 1.0 O2 A:8661 3.9 42.0 1.0 O3 A:8661 4.2 56.3 1.0 N1 A:8661 4.2 65.3 1.0 SG A:CYS736 4.3 72.7 1.0 SD A:MET601 4.6 55.9 1.0 C17 A:8661 4.6 58.9 1.0 CD1 A:LEU753 4.7 61.7 1.0 C7 A:8661 4.8 42.4 1.0 CE3 A:TRP600 4.9 49.4 1.0 OD1 A:ASN564 5.0 68.4 1.0

Fluorine binding site 4 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:57.9 occ:1.00 F4 A:8661 0.0 57.9 1.0 C16 A:8661 1.3 52.4 1.0 F3 A:8661 2.2 50.5 1.0 F2 A:8661 2.2 53.8 1.0 C4 A:8661 2.3 50.9 1.0 C3 A:8661 2.6 50.6 1.0 O1 A:8661 2.9 51.2 1.0 OD1 A:ASN564 3.2 68.4 1.0 CD1 A:LEU753 3.5 61.7 1.0 C5 A:8661 3.6 53.0 1.0 CE2 A:PHE749 3.8 72.0 1.0 SG A:CYS736 4.0 72.7 1.0 N1 A:8661 4.0 65.3 1.0 CG A:ASN564 4.1 71.1 1.0 CD2 A:PHE749 4.2 64.0 1.0 N2 A:8661 4.2 45.4 1.0 CD2 A:LEU753 4.3 75.2 1.0 CA A:ASN564 4.4 66.0 1.0 CH2 A:TRP600 4.5 60.8 1.0 CG A:LEU753 4.5 69.4 1.0 CZ3 A:TRP600 4.6 58.3 1.0 C2 A:8661 4.8 59.2 1.0 CB A:ASN564 4.8 73.4 1.0 CD1 A:ILE757 4.9 60.3 1.0 C17 A:8661 4.9 58.9 1.0 CZ A:PHE749 4.9 75.1 1.0 O3 A:8661 5.0 56.3 1.0

Fluorine binding site 5 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:59.9 occ:1.00 F1 B:8662 0.0 59.9 1.0 C13 B:8662 1.3 63.9 1.0 C14 B:8662 2.3 50.8 1.0 C12 B:8662 2.3 67.3 1.0 NH2 B:ARG611 3.1 68.4 0.5 CZ B:ARG611 3.3 72.0 0.5 CG B:ARG611 3.5 62.9 0.5 C15 B:8662 3.6 56.8 1.0 C11 B:8662 3.6 61.1 1.0 CB B:ALA607 3.6 34.2 1.0 NH1 B:ARG611 3.6 72.2 0.5 C B:ALA607 3.7 54.6 1.0 O B:ALA607 3.7 53.3 1.0 NE B:ARG611 3.8 73.2 0.5 N B:LEU608 3.9 56.0 1.0 C10 B:8662 4.0 53.2 1.0 CD B:ARG611 4.2 67.1 0.5 CA B:LEU608 4.3 58.1 1.0 CA B:ALA607 4.3 45.1 1.0 O B:HOH30 4.4 65.5 1.0 O B:HOH47 4.4 74.1 1.0 NE2 B:GLN570 4.5 59.5 1.0 CB B:ARG611 4.6 59.4 0.5 O B:HOH21 4.8 53.0 1.0 OE1 B:GLN570 4.9 56.7 1.0 CB B:LEU608 5.0 50.1 1.0 CD B:GLN570 5.0 53.8 1.0

Fluorine binding site 6 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:48.7 occ:1.00 F2 B:8662 0.0 48.7 1.0 C16 B:8662 1.3 51.4 1.0 F3 B:8662 2.2 50.0 1.0 F4 B:8662 2.2 51.7 1.0 C4 B:8662 2.4 52.2 1.0 N2 B:8662 2.5 43.6 1.0 O1 B:8662 2.8 53.2 1.0 C5 B:8662 2.9 51.6 1.0 C6 B:8662 3.4 42.5 1.0 C3 B:8662 3.7 49.3 1.0 O B:LEU563 3.7 66.7 1.0 CA B:GLY567 3.8 43.5 1.0 C7 B:8662 4.0 35.8 1.0 O2 B:8662 4.1 43.9 1.0 C8 B:8662 4.2 35.4 1.0 CZ3 B:TRP600 4.4 50.6 1.0 OD1 B:ASN564 4.4 68.1 1.0 CA B:ASN564 4.5 56.9 1.0 C B:LEU563 4.5 69.4 1.0 N B:GLY567 4.6 48.1 1.0 C B:GLY567 4.6 51.2 1.0 N B:ASN564 4.9 62.2 1.0 N1 B:8662 4.9 63.8 1.0 O B:ASN564 4.9 57.0 1.0 CG B:LEU753 4.9 69.8 1.0 CH2 B:TRP600 5.0 50.1 1.0

Fluorine binding site 7 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:50.0 occ:1.00 F3 B:8662 0.0 50.0 1.0 C16 B:8662 1.3 51.4 1.0 F4 B:8662 2.1 51.7 1.0 F2 B:8662 2.2 48.7 1.0 C4 B:8662 2.4 52.2 1.0 C3 B:8662 2.8 49.3 1.0 C5 B:8662 2.9 51.6 1.0 CE B:MET601 3.4 57.0 1.0 N2 B:8662 3.5 43.6 1.0 O1 B:8662 3.6 53.2 1.0 CZ3 B:TRP600 3.6 50.6 1.0 CH2 B:TRP600 3.7 50.1 1.0 SG B:CYS736 3.9 69.9 1.0 C6 B:8662 4.1 42.5 1.0 N1 B:8662 4.1 63.8 1.0 O2 B:8662 4.2 43.9 1.0 O3 B:8662 4.2 57.4 1.0 C17 B:8662 4.6 62.0 1.0 SD B:MET601 4.7 53.3 1.0 OD1 B:ASN564 4.8 68.1 1.0 CB B:CYS736 4.8 62.7 1.0 CE3 B:TRP600 4.9 50.6 1.0

Fluorine binding site 8 out of 8 in the Glucocorticoid Receptor Lbd Bound to GSK866


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Glucocorticoid Receptor Lbd Bound to GSK866 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:51.7 occ:1.00 F4 B:8662 0.0 51.7 1.0 C16 B:8662 1.3 51.4 1.0 F3 B:8662 2.1 50.0 1.0 F2 B:8662 2.2 48.7 1.0 C4 B:8662 2.3 52.2 1.0 O1 B:8662 2.7 53.2 1.0 C3 B:8662 2.8 49.3 1.0 OD1 B:ASN564 3.0 68.1 1.0 C5 B:8662 3.7 51.6 1.0 CE2 B:PHE749 3.9 64.5 1.0 CG B:ASN564 3.9 65.0 1.0 N2 B:8662 4.1 43.6 1.0 CA B:ASN564 4.1 56.9 1.0 CD2 B:PHE749 4.1 61.5 1.0 N1 B:8662 4.2 63.8 1.0 SG B:CYS736 4.3 69.9 1.0 CG B:LEU753 4.4 69.8 1.0 CB B:ASN564 4.5 61.0 1.0 O B:LEU563 4.7 66.7 1.0 CZ3 B:TRP600 4.7 50.6 1.0 CH2 B:TRP600 4.7 50.1 1.0 C2 B:8662 4.8 63.3 1.0 N B:ASN564 4.8 62.2 1.0 CD1 B:LEU753 4.8 66.9 1.0 ND2 B:ASN564 4.9 59.8 1.0 O B:ASN564 4.9 57.0 1.0

K.P.Madauss, R.K.Bledsoe, I.Mclay, E.L.Stewart, I.J.Uings, G.Weingarten, S.P.Williams. The First X-Ray Crystal Structure of the Glucocorticoid Receptor Bound to A Non-Steroidal Agonist. Bioorg.Med.Chem.Lett. V. 18 6097 2008.
ISSN: ISSN 0960-894X
PubMed: 18952422
DOI: 10.1016/J.BMCL.2008.10.021