Fluorine in PDB 8fb1: Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket, PDB code: 8fb1 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)	56.78 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.16, 96.486, 56.797, 90, 91.3, 90
R / Rfree (%)	20.6 / 25.3

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Fluorine atom in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket (pdb code 8fb1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 19 binding sites of Fluorine where determined in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket, PDB code: 8fb1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:33.1 occ:1.00 F9 A:XNR601 0.0 33.1 1.0 C3 A:XNR601 1.3 30.1 1.0 C4 A:XNR601 2.3 30.2 1.0 C2 A:XNR601 2.4 30.2 1.0 OG A:SER404 2.8 24.4 1.0 CB A:MET365 3.4 23.7 1.0 CB A:SER404 3.5 22.6 1.0 C5 A:XNR601 3.6 29.7 1.0 C1 A:XNR601 3.7 30.8 1.0 O A:MET365 3.7 23.8 1.0 CG1 A:VAL376 4.0 22.3 1.0 SD A:MET365 4.0 27.1 1.0 C A:MET365 4.0 22.8 1.0 CG A:MET365 4.1 24.9 1.0 CG2 A:ILE400 4.1 16.2 1.0 C6 A:XNR601 4.2 29.2 1.0 CA A:MET365 4.3 23.3 1.0 CB A:TYR369 4.3 21.2 1.0 O A:ILE400 4.4 19.5 1.0 CD1 A:TYR369 4.6 20.8 1.0 CB A:VAL376 4.8 21.5 1.0 N A:CYS366 4.8 22.3 1.0 N10 A:XNR601 4.8 38.1 1.0 C8 A:XNR601 4.9 28.8 1.0 CG A:TYR369 4.9 20.5 1.0 C A:ILE400 4.9 18.8 1.0 CA A:SER404 5.0 22.0 1.0

Fluorine binding site 2 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:54.7 occ:1.00 F33 A:XNR601 0.0 54.7 1.0 C25 A:XNR601 1.3 52.4 1.0 C24 A:XNR601 2.4 50.5 1.0 C26 A:XNR601 2.4 46.1 1.0 N A:LEU324 3.0 16.3 1.0 CB A:HIS323 3.0 18.3 1.0 C A:HIS323 3.2 16.6 1.0 CG A:LEU324 3.4 16.4 1.0 CD2 A:LEU324 3.5 17.1 1.0 C17 A:XNR601 3.6 33.5 1.0 CA A:LEU324 3.6 16.6 1.0 O A:HIS323 3.6 15.9 1.0 O A:CYS320 3.6 19.5 1.0 C23 A:XNR601 3.7 47.0 1.0 CA A:HIS323 3.7 17.9 1.0 C27 A:XNR601 3.7 45.1 1.0 CB A:LEU324 4.0 17.0 1.0 C21 A:XNR601 4.2 46.2 1.0 CG A:HIS323 4.3 20.3 1.0 N A:HIS323 4.6 19.0 1.0 CD1 A:LEU324 4.6 16.2 1.0 C A:CYS320 4.6 19.6 1.0 ND1 A:HIS323 4.7 21.6 1.0 CA A:CYS320 4.9 20.1 1.0

Fluorine binding site 3 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:36.5 occ:1.00 F4 A:4Y5602 0.0 36.5 1.0 C16 A:4Y5602 1.3 29.6 1.0 C17 A:4Y5602 2.4 28.9 1.0 C15 A:4Y5602 2.4 28.7 1.0 C6 A:4Y5602 2.8 28.5 1.0 F A:4Y5602 2.9 27.4 1.0 C4 A:4Y5602 3.1 26.1 1.0 C5 A:4Y5602 3.2 26.2 1.0 O A:LEU501 3.5 19.4 1.0 CG A:LEU501 3.5 17.9 1.0 CB A:LEU505 3.6 28.4 1.0 CG A:LEU505 3.6 28.8 1.0 CA A:TYR502 3.7 21.3 1.0 C18 A:4Y5602 3.7 30.6 1.0 C20 A:4Y5602 3.7 28.7 1.0 N A:TYR502 3.7 20.8 1.0 C A:LEU501 3.7 19.7 1.0 CD2 A:LEU505 3.7 30.0 1.0 N A:4Y5602 3.8 28.4 1.0 CD2 A:LEU501 4.1 18.5 1.0 CE1 A:PHE506 4.1 22.9 1.0 C19 A:4Y5602 4.2 29.2 1.0 CD1 A:LEU501 4.3 18.4 1.0 C3 A:4Y5602 4.3 27.5 1.0 CB A:LEU501 4.4 18.3 1.0 CD1 A:PHE506 4.4 22.5 1.0 C A:4Y5602 4.5 27.1 1.0 C A:TYR502 4.6 22.2 1.0 N1 A:4Y5602 4.6 30.1 1.0 O A:TYR502 4.7 20.7 1.0 CB A:TYR502 4.7 21.0 1.0 CA A:LEU501 4.7 18.1 1.0 CA A:LEU505 4.9 28.6 1.0 C21 A:4Y5602 4.9 31.2 1.0 N A:LEU505 4.9 28.6 1.0

Fluorine binding site 4 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:27.4 occ:1.00 F A:4Y5602 0.0 27.4 1.0 C5 A:4Y5602 1.3 26.2 1.0 C A:4Y5602 2.4 27.1 1.0 C4 A:4Y5602 2.4 26.1 1.0 F4 A:4Y5602 2.9 36.5 1.0 CD2 A:LEU501 3.2 18.5 1.0 C6 A:4Y5602 3.2 28.5 1.0 C16 A:4Y5602 3.2 29.6 1.0 C15 A:4Y5602 3.3 28.7 1.0 CG2 A:ILE328 3.4 16.7 1.0 CG A:LEU501 3.4 17.9 1.0 C1 A:4Y5602 3.7 25.5 1.0 CD1 A:LEU501 3.7 18.4 1.0 C3 A:4Y5602 3.7 27.5 1.0 C17 A:4Y5602 4.1 28.9 1.0 C2 A:4Y5602 4.2 23.8 1.0 CD2 A:LEU505 4.3 30.0 1.0 CB A:ALA357 4.3 18.9 1.0 N A:4Y5602 4.4 28.4 1.0 CG A:LEU505 4.4 28.8 1.0 C20 A:4Y5602 4.4 28.7 1.0 O A:LEU353 4.5 18.9 1.0 CD1 A:ILE328 4.6 18.0 1.0 N1 A:4Y5602 4.7 30.1 1.0 CB A:ILE328 4.7 17.1 1.0 CB A:LEU501 4.9 18.3 1.0 CG1 A:ILE328 4.9 17.8 1.0 CG2 A:VAL332 5.0 17.1 1.0

Fluorine binding site 5 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 5 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:34.5 occ:1.00 F1 A:4Y5602 0.0 34.5 1.0 C14 A:4Y5602 1.4 29.9 1.0 F3 A:4Y5602 2.2 30.4 1.0 F2 A:4Y5602 2.2 32.0 1.0 C9 A:4Y5602 2.4 29.5 1.0 C10 A:4Y5602 2.7 30.2 1.0 NE2 A:GLN484 3.2 31.3 1.0 CB A:GLN487 3.4 17.2 1.0 CG A:GLN487 3.4 16.5 1.0 C8 A:4Y5602 3.7 29.7 1.0 CE2 A:PHE506 3.9 23.0 1.0 CZ A:PHE506 4.0 23.9 1.0 CD A:GLN484 4.0 29.8 1.0 CD2 A:PHE506 4.1 22.9 1.0 O A:LEU483 4.1 18.6 1.0 CA A:GLN484 4.1 21.6 1.0 C11 A:4Y5602 4.2 28.3 1.0 O A:LEU505 4.2 29.9 1.0 CD A:GLN487 4.2 16.1 1.0 CE1 A:PHE506 4.3 22.9 1.0 C7 A:4Y5602 4.4 30.4 1.0 CG A:GLN484 4.4 25.9 1.0 C A:LEU483 4.5 18.5 1.0 N A:GLN484 4.5 19.3 1.0 CG A:PHE506 4.5 23.4 1.0 OE1 A:GLN487 4.6 16.1 1.0 CD1 A:PHE506 4.6 22.5 1.0 O A:4Y5602 4.7 33.0 1.0 CB A:GLN484 4.8 23.2 1.0 OE1 A:GLN484 4.8 31.0 1.0 C13 A:4Y5602 4.9 27.1 1.0 CA A:GLN487 4.9 18.4 1.0 C A:LEU505 5.0 28.2 1.0

Fluorine binding site 6 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 6 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:32.0 occ:1.00 F2 A:4Y5602 0.0 32.0 1.0 C14 A:4Y5602 1.4 29.9 1.0 F1 A:4Y5602 2.2 34.5 1.0 F3 A:4Y5602 2.2 30.4 1.0 C9 A:4Y5602 2.4 29.5 1.0 C7 A:4Y5602 2.8 30.4 1.0 C8 A:4Y5602 3.0 29.7 1.0 O A:4Y5602 3.2 33.0 1.0 N1 A:4Y5602 3.3 30.1 1.0 C10 A:4Y5602 3.6 30.2 1.0 CE1 A:PHE506 3.7 22.9 1.0 N A:4Y5602 3.7 28.4 1.0 NE2 A:GLN484 3.8 31.3 1.0 O A:LEU505 3.8 29.9 1.0 CB A:LEU505 3.8 28.4 1.0 CZ A:PHE506 3.9 23.9 1.0 CD A:GLN484 3.9 29.8 1.0 C3 A:4Y5602 4.1 27.5 1.0 CD1 A:PHE506 4.1 22.5 1.0 C A:LEU505 4.2 28.2 1.0 CD1 A:LEU505 4.3 28.6 1.0 OE1 A:GLN484 4.3 31.0 1.0 CG A:LEU505 4.3 28.8 1.0 C13 A:4Y5602 4.3 27.1 1.0 CG A:GLN484 4.5 25.9 1.0 CE2 A:PHE506 4.5 23.0 1.0 CA A:LEU505 4.6 28.6 1.0 C6 A:4Y5602 4.6 28.5 1.0 CG A:PHE506 4.7 23.4 1.0 C2 A:4Y5602 4.7 23.8 1.0 C11 A:4Y5602 4.8 28.3 1.0 CD2 A:PHE506 4.8 22.9 1.0 C4 A:4Y5602 4.8 26.1 1.0

Fluorine binding site 7 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 7 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:30.4 occ:1.00 F3 A:4Y5602 0.0 30.4 1.0 C14 A:4Y5602 1.4 29.9 1.0 F1 A:4Y5602 2.2 34.5 1.0 F2 A:4Y5602 2.2 32.0 1.0 C9 A:4Y5602 2.4 29.5 1.0 O A:4Y5602 3.1 33.0 1.0 C8 A:4Y5602 3.2 29.7 1.0 CB A:LEU483 3.3 17.4 1.0 N A:GLN484 3.3 19.3 1.0 C7 A:4Y5602 3.3 30.4 1.0 C10 A:4Y5602 3.3 30.2 1.0 C A:LEU483 3.3 18.5 1.0 CG A:GLN484 3.5 25.9 1.0 CA A:GLN484 3.6 21.6 1.0 O A:LEU483 3.6 18.6 1.0 NE2 A:GLN484 3.7 31.3 1.0 CD A:GLN484 3.7 29.8 1.0 CA A:LEU483 3.9 17.7 1.0 O A:VAL480 4.0 19.4 1.0 CB A:GLN484 4.1 23.2 1.0 N1 A:4Y5602 4.4 30.1 1.0 C13 A:4Y5602 4.4 27.1 1.0 CG A:LEU483 4.5 17.1 1.0 CD1 A:LEU483 4.5 17.6 1.0 OE1 A:GLN484 4.5 31.0 1.0 C11 A:4Y5602 4.6 28.3 1.0 CG1 A:VAL480 4.6 17.8 1.0 CB A:GLN487 4.7 17.2 1.0 N A:LEU483 5.0 16.6 1.0 C A:GLN484 5.0 20.8 1.0 C A:VAL480 5.0 18.1 1.0 C12 A:4Y5602 5.0 28.2 1.0

Fluorine binding site 8 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 8 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:64.4 occ:1.00 F4 A:4Y5603 0.0 64.4 1.0 C16 A:4Y5603 1.4 64.4 1.0 C17 A:4Y5603 2.4 67.4 1.0 C15 A:4Y5603 2.4 63.1 1.0 C6 A:4Y5603 2.8 58.7 1.0 N A:4Y5603 3.1 58.6 1.0 F3 A:4Y5603 3.3 81.7 1.0 CE A:LYS456 3.7 26.8 1.0 C18 A:4Y5603 3.7 72.0 1.0 C20 A:4Y5603 3.7 63.8 1.0 C4 A:4Y5603 3.9 57.8 1.0 CG A:LYS456 4.1 22.8 1.0 N1 A:4Y5603 4.2 60.2 1.0 C19 A:4Y5603 4.2 68.5 1.0 CD A:LYS456 4.4 24.9 1.0 C14 A:4Y5603 4.6 76.8 1.0 NZ A:LYS456 4.6 29.5 1.0 C3 A:4Y5603 4.6 56.8 1.0 C5 A:4Y5603 4.8 50.6 1.0 F A:4Y5603 4.8 48.3 1.0 C9 A:4Y5603 4.9 74.2 1.0 C21 A:4Y5603 4.9 77.1 1.0

Fluorine binding site 9 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 9 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:48.3 occ:1.00 F A:4Y5603 0.0 48.3 1.0 C5 A:4Y5603 1.3 50.6 1.0 C A:4Y5603 2.4 49.1 1.0 C4 A:4Y5603 2.4 57.8 1.0 C6 A:4Y5603 3.2 58.7 1.0 C20 A:4Y5603 3.2 63.8 1.0 C15 A:4Y5603 3.2 63.1 1.0 O B:GLN460 3.5 18.7 1.0 CB B:GLN460 3.6 22.8 1.0 C1 A:4Y5603 3.7 51.9 1.0 C3 A:4Y5603 3.7 56.8 1.0 CA A:LYS456 3.7 18.6 1.0 C B:GLN460 4.0 20.5 1.0 C19 A:4Y5603 4.0 68.5 1.0 O A:CYS455 4.1 16.0 1.0 C16 A:4Y5603 4.2 64.4 1.0 C2 A:4Y5603 4.2 54.3 1.0 O A:LYS456 4.2 16.8 1.0 N A:4Y5603 4.4 58.6 1.0 CA B:GLN460 4.4 21.4 1.0 N A:LYS456 4.4 17.5 1.0 C A:LYS456 4.5 16.8 1.0 CG A:LYS456 4.5 22.8 1.0 CB A:LYS456 4.5 20.7 1.0 C A:CYS455 4.5 17.7 1.0 CD1 B:LEU463 4.7 29.0 1.0 N1 A:4Y5603 4.7 60.2 1.0 CG B:GLN460 4.7 24.9 1.0 N B:SER461 4.7 20.0 1.0 C18 A:4Y5603 4.8 72.0 1.0 F4 A:4Y5603 4.8 64.4 1.0 SG A:CYS455 4.9 18.1 1.0 C17 A:4Y5603 4.9 67.4 1.0 NE2 B:GLN460 4.9 21.6 1.0 NE2 A:HIS458 4.9 19.2 1.0

Fluorine binding site 10 out of 19 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A 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 10 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:87.1 occ:1.00 F1 A:4Y5603 0.0 87.1 1.0 C14 A:4Y5603 1.4 76.8 1.0 F3 A:4Y5603 2.3 81.7 1.0 F2 A:4Y5603 2.3 77.4 1.0 C9 A:4Y5603 2.4 74.2 1.0 C10 A:4Y5603 2.7 74.6 1.0 OE1 A:GLU271 3.4 28.1 1.0 OE2 A:GLU271 3.5 25.3 1.0 CD A:GLU271 3.6 23.8 1.0 C8 A:4Y5603 3.8 69.5 1.0 NZ A:LYS456 3.9 29.5 1.0 C11 A:4Y5603 4.2 71.4 1.0 C7 A:4Y5603 4.4 65.6 1.0 CE A:LYS456 4.6 26.8 1.0 CG A:GLU271 4.7 21.8 1.0 C13 A:4Y5603 4.9 71.5 1.0 O A:4Y5603 5.0 67.2 1.0 N1 A:4Y5603 5.0 60.2 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