Fluorine in PDB 8fb2: Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket, PDB code: 8fb2 was solved by F.F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.53 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.6, 97.68, 56.81, 90, 91.43, 90
R / Rfree (%)	17.9 / 23

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket (pdb code 8fb2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket, PDB code: 8fb2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F4001 b:44.6 occ:1.00 F1 A:XO54001 0.0 44.6 1.0 C5 A:XO54001 1.3 40.7 1.0 C4 A:XO54001 2.3 37.9 1.0 C6 A:XO54001 2.3 39.2 1.0 H5 A:XO54001 2.6 37.8 0.0 H6 A:XO54001 2.6 39.2 0.0 OG A:SER404 2.9 45.0 1.0 CB A:MET365 3.5 35.6 1.0 C3 A:XO54001 3.6 38.3 1.0 C7 A:XO54001 3.6 42.3 1.0 CB A:SER404 3.6 38.6 1.0 O A:MET365 3.7 34.5 1.0 CG1 A:VAL376 3.8 36.7 1.0 SD A:MET365 3.9 41.7 1.0 C A:MET365 4.0 36.6 1.0 C2 A:XO54001 4.1 39.6 1.0 CG A:MET365 4.2 38.5 1.0 CG2 A:ILE400 4.3 34.6 1.0 CB A:TYR369 4.3 41.0 1.0 CA A:MET365 4.3 33.5 1.0 O A:HOH4128 4.5 46.0 1.0 CD1 A:TYR369 4.6 45.4 1.0 O A:ILE400 4.6 37.0 1.0 H18 A:XO54001 4.7 43.5 0.0 CB A:VAL376 4.7 37.2 1.0 H20 A:XO54001 4.7 40.5 0.0 N1 A:XO54001 4.8 46.8 1.0 C15 A:XO54001 4.8 40.5 1.0 N A:CYS366 4.8 34.9 1.0 CG A:TYR369 4.9 42.6 1.0

Fluorine binding site 2 out of 4 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F4002 b:31.7 occ:1.00 F1 A:XNX4002 0.0 31.7 1.0 C5 A:XNX4002 1.4 34.5 1.0 C6 A:XNX4002 2.3 36.3 1.0 C4 A:XNX4002 2.4 32.8 1.0 C16 A:XNX4002 3.1 32.9 1.0 C7 A:XNX4002 3.1 34.8 1.0 CD2 A:LEU501 3.3 45.4 1.0 C15 A:XNX4002 3.3 32.8 1.0 CG2 A:ILE328 3.5 33.7 1.0 C1 A:XNX4002 3.6 34.1 1.0 C3 A:XNX4002 3.6 34.4 1.0 CG A:LEU501 3.6 43.7 1.0 CD1 A:LEU501 3.7 42.8 1.0 CD2 A:LEU505 3.9 60.1 1.0 C17 A:XNX4002 4.1 35.0 1.0 C2 A:XNX4002 4.1 31.6 1.0 CG A:LEU505 4.3 60.6 1.0 CB A:ALA357 4.3 33.3 1.0 N1 A:XNX4002 4.4 33.6 1.0 O A:LEU353 4.4 32.4 1.0 C20 A:XNX4002 4.5 24.5 1.0 CD1 A:ILE328 4.5 29.7 1.0 N2 A:XNX4002 4.6 39.0 1.0 CB A:ILE328 4.8 30.8 1.0 CG1 A:ILE328 4.9 29.9 1.0 C A:LEU353 4.9 34.3 1.0

Fluorine binding site 3 out of 4 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F4000 b:53.5 occ:1.00 F1 B:XO54000 0.0 53.5 1.0 C5 B:XO54000 1.3 48.7 1.0 C4 B:XO54000 2.3 48.1 1.0 C6 B:XO54000 2.4 46.6 1.0 H5 B:XO54000 2.6 48.2 0.0 H6 B:XO54000 2.6 46.7 0.0 OG B:SER404 2.8 47.9 1.0 CB B:MET365 3.4 38.7 1.0 C3 B:XO54000 3.6 46.8 1.0 C7 B:XO54000 3.6 47.7 1.0 O B:MET365 3.7 42.3 1.0 CB B:SER404 3.7 38.0 1.0 SD B:MET365 3.9 49.3 1.0 CG1 B:VAL376 3.9 39.4 1.0 C B:MET365 4.1 42.3 1.0 CG B:MET365 4.1 43.2 1.0 C2 B:XO54000 4.1 46.6 1.0 CG2 B:ILE400 4.2 37.3 1.0 CA B:MET365 4.3 36.6 1.0 CB B:TYR369 4.3 42.4 1.0 H19 B:XO54000 4.6 47.0 0.0 O B:ILE400 4.6 44.0 1.0 CD1 B:TYR369 4.7 46.4 1.0 H20 B:XO54000 4.8 47.9 0.0 CB B:VAL376 4.8 39.9 1.0 N1 B:XO54000 4.8 52.7 1.0 C15 B:XO54000 4.8 47.9 1.0 N B:CYS366 4.9 41.1 1.0 CG B:TYR369 4.9 44.3 1.0

Fluorine binding site 4 out of 4 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 8 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F4001 b:34.9 occ:1.00 F1 B:XNX4001 0.0 34.9 1.0 C5 B:XNX4001 1.4 31.8 1.0 C6 B:XNX4001 2.3 29.3 1.0 C4 B:XNX4001 2.4 33.6 1.0 C20 B:XNX4001 3.0 33.2 1.0 C7 B:XNX4001 3.1 34.7 1.0 C15 B:XNX4001 3.3 34.2 1.0 CD2 B:LEU501 3.3 37.3 1.0 CG2 B:ILE328 3.5 28.3 1.0 C1 B:XNX4001 3.6 28.0 1.0 CG B:LEU501 3.6 37.5 1.0 C3 B:XNX4001 3.6 32.6 1.0 CD1 B:LEU501 3.7 36.1 1.0 CD2 B:LEU505 3.9 56.5 1.0 C19 B:XNX4001 4.0 33.8 1.0 C2 B:XNX4001 4.1 29.1 1.0 CB B:ALA357 4.2 29.6 1.0 CG B:LEU505 4.3 54.9 1.0 N1 B:XNX4001 4.4 35.4 1.0 O B:LEU353 4.4 35.7 1.0 C16 B:XNX4001 4.5 33.5 1.0 CD1 B:ILE328 4.5 30.4 1.0 N2 B:XNX4001 4.6 36.2 1.0 CB B:ILE328 4.8 32.3 1.0 CG1 B:ILE328 4.9 30.6 1.0 C B:LEU353 4.9 36.7 1.0

M.E.Schnute, J.I.Trujillo, K.L.Lee, R.Unwalla, F.F.Vajdos, B.Kauppi, P.Nuhant, A.C.Flick, K.K.Crouse, Y.Zhao, A.Samuel, V.Lombardo, A.P.Taylor, A.L.Brault, J.D.Knafels, M.L.Vazquez, G.Berstein. Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists. Acs Med.Chem.Lett. V. 14 191 2023.
ISSN: ISSN 1948-5875
PubMed: 36793423
DOI: 10.1021/ACSMEDCHEMLETT.2C00500