Fluorine in PDB 8fav: Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 Andindazole Acid Bound in H12- Pocket

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 Andindazole Acid Bound in H12- Pocket, PDB code: 8fav 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)	56.90 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.088, 96.922, 56.914, 90, 91.26, 90
R / Rfree (%)	19.2 / 23.3

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 Andindazole Acid Bound in H12- Pocket also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 Andindazole Acid Bound in H12- Pocket (pdb code 8fav). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 Andindazole Acid Bound in H12- Pocket, PDB code: 8fav:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:25.3 occ:1.00 F22 A:LKY601 0.0 25.3 1.0 C21 A:LKY601 1.3 25.3 1.0 C20 A:LKY601 2.4 25.0 1.0 C23 A:LKY601 2.4 22.9 1.0 OG A:SER404 2.9 30.4 1.0 CB A:MET365 3.4 23.8 1.0 O A:MET365 3.5 21.3 1.0 C3 A:LKY601 3.6 23.7 1.0 CB A:SER404 3.6 27.1 1.0 C24 A:LKY601 3.7 23.9 1.0 CG1 A:VAL376 3.8 19.5 1.0 C A:MET365 3.9 21.6 1.0 CB A:TYR369 4.1 24.0 1.0 C1 A:LKY601 4.2 23.1 1.0 SD A:MET365 4.2 30.0 1.0 CA A:MET365 4.2 22.8 1.0 CG A:MET365 4.3 24.9 1.0 CG2 A:ILE400 4.3 23.1 1.0 CD1 A:TYR369 4.5 25.2 1.0 CB A:VAL376 4.6 21.8 1.0 N A:CYS366 4.7 22.6 1.0 O A:ILE400 4.7 22.2 1.0 CG A:TYR369 4.7 25.6 1.0 N25 A:LKY601 4.8 21.0 1.0 CA A:TYR369 4.9 23.9 1.0 C4 A:LKY601 4.9 23.6 1.0 O27 A:LKY601 4.9 22.4 1.0 N A:TYR369 5.0 23.5 1.0

Fluorine binding site 2 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:21.6 occ:1.00 F4 A:4Y5602 0.0 21.6 1.0 C16 A:4Y5602 1.3 19.4 1.0 C17 A:4Y5602 2.3 19.5 1.0 C15 A:4Y5602 2.4 18.4 1.0 C6 A:4Y5602 2.8 19.5 1.0 F A:4Y5602 2.9 20.8 1.0 C4 A:4Y5602 3.1 20.1 1.0 C5 A:4Y5602 3.2 20.0 1.0 CB A:LEU505 3.5 38.2 1.0 CG A:LEU501 3.6 23.2 1.0 CG A:LEU505 3.6 39.7 1.0 O A:LEU501 3.6 24.0 1.0 C18 A:4Y5602 3.7 16.6 1.0 C20 A:4Y5602 3.7 18.4 1.0 CA A:TYR502 3.7 25.2 1.0 N A:4Y5602 3.8 22.4 1.0 N A:TYR502 3.8 24.1 1.0 C A:LEU501 3.8 25.8 1.0 CD2 A:LEU505 3.9 39.1 1.0 CE1 A:PHE506 4.1 30.6 1.0 C19 A:4Y5602 4.2 17.4 1.0 CD2 A:LEU501 4.2 22.5 1.0 C3 A:4Y5602 4.2 21.9 1.0 CD1 A:LEU501 4.3 23.1 1.0 C A:4Y5602 4.4 20.8 1.0 CD1 A:PHE506 4.4 29.5 1.0 CB A:LEU501 4.5 24.2 1.0 N1 A:4Y5602 4.5 23.1 1.0 O A:TYR502 4.6 27.5 1.0 C A:TYR502 4.6 26.9 1.0 CB A:TYR502 4.7 25.0 1.0 CA A:LEU501 4.8 23.2 1.0 CA A:LEU505 4.8 39.2 1.0 C21 A:4Y5602 4.8 20.9 1.0 N A:LEU505 4.9 35.9 1.0

Fluorine binding site 3 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:20.8 occ:1.00 F A:4Y5602 0.0 20.8 1.0 C5 A:4Y5602 1.3 20.0 1.0 C A:4Y5602 2.4 20.8 1.0 C4 A:4Y5602 2.4 20.1 1.0 F4 A:4Y5602 2.9 21.6 1.0 C16 A:4Y5602 3.2 19.4 1.0 C6 A:4Y5602 3.2 19.5 1.0 CD2 A:LEU501 3.3 22.5 1.0 C15 A:4Y5602 3.3 18.4 1.0 CG2 A:ILE328 3.4 17.7 1.0 CG A:LEU501 3.5 23.2 1.0 C1 A:4Y5602 3.6 24.0 1.0 C3 A:4Y5602 3.7 21.9 1.0 CD1 A:LEU501 3.7 23.1 1.0 C17 A:4Y5602 4.1 19.5 1.0 C2 A:4Y5602 4.2 19.9 1.0 CB A:ALA357 4.3 22.3 1.0 CD2 A:LEU505 4.4 39.1 1.0 CG A:LEU505 4.4 39.7 1.0 N A:4Y5602 4.4 22.4 1.0 C20 A:4Y5602 4.4 18.4 1.0 CD1 A:ILE328 4.5 21.1 1.0 O A:LEU353 4.6 20.1 1.0 N1 A:4Y5602 4.7 23.1 1.0 CB A:ILE328 4.7 18.6 1.0 CG1 A:ILE328 4.9 18.6 1.0 CG2 A:VAL332 4.9 19.2 1.0

Fluorine binding site 4 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:30.9 occ:1.00 F1 A:4Y5602 0.0 30.9 1.0 C14 A:4Y5602 1.4 28.7 1.0 F2 A:4Y5602 2.2 28.3 1.0 F3 A:4Y5602 2.2 33.0 1.0 C9 A:4Y5602 2.4 28.0 1.0 C10 A:4Y5602 2.8 26.6 1.0 OE1 A:GLN484 3.1 45.3 1.0 CB A:GLN487 3.4 25.9 1.0 CG A:GLN487 3.4 24.6 1.0 CD A:GLN484 3.7 39.1 1.0 CE2 A:PHE506 3.8 34.1 1.0 C8 A:4Y5602 3.8 29.6 1.0 CZ A:PHE506 4.0 33.3 1.0 CD2 A:PHE506 4.0 33.7 1.0 CA A:GLN484 4.2 23.7 1.0 O A:LEU483 4.2 23.3 1.0 C11 A:4Y5602 4.2 28.2 1.0 O A:LEU505 4.2 37.5 1.0 CD A:GLN487 4.3 23.9 1.0 CG A:GLN484 4.3 30.6 1.0 C7 A:4Y5602 4.4 26.1 1.0 NE2 A:GLN484 4.4 40.7 1.0 CE1 A:PHE506 4.4 30.6 1.0 CG A:PHE506 4.4 32.5 1.0 C A:LEU483 4.5 22.6 1.0 N A:GLN484 4.5 22.7 1.0 OE1 A:GLN487 4.6 26.3 1.0 CD1 A:PHE506 4.7 29.5 1.0 O A:4Y5602 4.7 30.0 1.0 CB A:GLN484 4.8 26.7 1.0 C13 A:4Y5602 4.9 24.9 1.0 CA A:GLN487 4.9 27.7 1.0

Fluorine binding site 5 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:28.3 occ:1.00 F2 A:4Y5602 0.0 28.3 1.0 C14 A:4Y5602 1.4 28.7 1.0 F3 A:4Y5602 2.2 33.0 1.0 F1 A:4Y5602 2.2 30.9 1.0 C9 A:4Y5602 2.4 28.0 1.0 C7 A:4Y5602 2.8 26.1 1.0 C8 A:4Y5602 2.9 29.6 1.0 O A:4Y5602 3.2 30.0 1.0 N1 A:4Y5602 3.3 23.1 1.0 C10 A:4Y5602 3.6 26.6 1.0 N A:4Y5602 3.7 22.4 1.0 O A:LEU505 3.8 37.5 1.0 CE1 A:PHE506 3.8 30.6 1.0 CD A:GLN484 3.9 39.1 1.0 CZ A:PHE506 3.9 33.3 1.0 OE1 A:GLN484 3.9 45.3 1.0 CB A:LEU505 3.9 38.2 1.0 NE2 A:GLN484 4.0 40.7 1.0 C3 A:4Y5602 4.1 21.9 1.0 CD1 A:PHE506 4.2 29.5 1.0 CD1 A:LEU505 4.2 41.2 1.0 C A:LEU505 4.3 40.0 1.0 C13 A:4Y5602 4.3 24.9 1.0 CE2 A:PHE506 4.4 34.1 1.0 CG A:GLN484 4.4 30.6 1.0 CG A:LEU505 4.5 39.7 1.0 C6 A:4Y5602 4.7 19.5 1.0 CG A:PHE506 4.7 32.5 1.0 CA A:LEU505 4.7 39.2 1.0 C2 A:4Y5602 4.7 19.9 1.0 CD2 A:PHE506 4.8 33.7 1.0 C11 A:4Y5602 4.8 28.2 1.0 C4 A:4Y5602 4.9 20.1 1.0

Fluorine binding site 6 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:33.0 occ:1.00 F3 A:4Y5602 0.0 33.0 1.0 C14 A:4Y5602 1.4 28.7 1.0 F2 A:4Y5602 2.2 28.3 1.0 F1 A:4Y5602 2.2 30.9 1.0 C9 A:4Y5602 2.4 28.0 1.0 O A:4Y5602 3.2 30.0 1.0 C8 A:4Y5602 3.2 29.6 1.0 N A:GLN484 3.3 22.7 1.0 CB A:LEU483 3.3 20.9 1.0 C10 A:4Y5602 3.4 26.6 1.0 C A:LEU483 3.4 22.6 1.0 C7 A:4Y5602 3.4 26.1 1.0 CG A:GLN484 3.4 30.6 1.0 CD A:GLN484 3.6 39.1 1.0 CA A:GLN484 3.6 23.7 1.0 O A:LEU483 3.7 23.3 1.0 OE1 A:GLN484 3.7 45.3 1.0 CA A:LEU483 4.0 19.3 1.0 O A:VAL480 4.1 20.3 1.0 CB A:GLN484 4.1 26.7 1.0 NE2 A:GLN484 4.3 40.7 1.0 N1 A:4Y5602 4.5 23.1 1.0 C13 A:4Y5602 4.5 24.9 1.0 CG1 A:VAL480 4.6 26.5 1.0 CG A:LEU483 4.6 18.9 1.0 C11 A:4Y5602 4.6 28.2 1.0 CD1 A:LEU483 4.6 20.4 1.0 CB A:GLN487 4.8 25.9 1.0 N A:LEU483 5.0 19.4 1.0 C A:GLN484 5.0 26.0 1.0

Fluorine binding site 7 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:29.1 occ:1.00 F22 B:LKY601 0.0 29.1 1.0 C21 B:LKY601 1.3 25.2 1.0 C20 B:LKY601 2.3 24.9 1.0 C23 B:LKY601 2.4 25.0 1.0 OG B:SER404 2.9 32.3 1.0 CB B:MET365 3.5 26.7 1.0 O B:MET365 3.6 24.4 1.0 CB B:SER404 3.6 28.4 1.0 C3 B:LKY601 3.6 26.3 1.0 C24 B:LKY601 3.7 24.2 1.0 CG1 B:VAL376 3.7 26.8 1.0 C B:MET365 4.0 24.3 1.0 CB B:TYR369 4.0 29.0 1.0 SD B:MET365 4.1 32.2 1.0 C1 B:LKY601 4.2 26.1 1.0 CG B:MET365 4.2 31.1 1.0 CA B:MET365 4.3 26.4 1.0 CD1 B:TYR369 4.3 28.8 1.0 CG2 B:ILE400 4.4 28.7 1.0 CB B:VAL376 4.5 27.6 1.0 CG B:TYR369 4.6 28.9 1.0 O B:ILE400 4.6 23.7 1.0 N B:CYS366 4.8 24.7 1.0 CA B:TYR369 4.8 29.2 1.0 C4 B:LKY601 4.9 25.4 1.0 N25 B:LKY601 4.9 26.8 1.0 N B:TYR369 4.9 27.7 1.0

Fluorine binding site 8 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:22.8 occ:1.00 F4 B:4Y5602 0.0 22.8 1.0 C16 B:4Y5602 1.4 18.8 1.0 C17 B:4Y5602 2.3 18.9 1.0 C15 B:4Y5602 2.4 18.7 1.0 F B:4Y5602 2.8 20.9 1.0 C6 B:4Y5602 2.8 20.5 1.0 C4 B:4Y5602 3.1 22.8 1.0 C5 B:4Y5602 3.3 21.2 1.0 CG B:LEU501 3.4 23.3 1.0 O B:LEU501 3.5 24.0 1.0 CB B:LEU505 3.6 31.5 1.0 CG B:LEU505 3.6 29.4 1.0 C18 B:4Y5602 3.7 18.7 1.0 CA B:TYR502 3.7 23.0 1.0 C B:LEU501 3.7 22.1 1.0 N B:TYR502 3.7 22.4 1.0 C20 B:4Y5602 3.7 19.6 1.0 N B:4Y5602 3.8 19.8 1.0 CD2 B:LEU505 3.9 30.0 1.0 CD2 B:LEU501 4.1 23.7 1.0 CD1 B:LEU501 4.1 22.2 1.0 C19 B:4Y5602 4.2 16.6 1.0 CE1 B:PHE506 4.2 28.8 1.0 C3 B:4Y5602 4.3 21.5 1.0 CB B:LEU501 4.4 23.8 1.0 C B:4Y5602 4.4 23.0 1.0 CD1 B:PHE506 4.5 27.5 1.0 O B:TYR502 4.6 26.0 1.0 C B:TYR502 4.6 25.6 1.0 N1 B:4Y5602 4.6 21.9 1.0 CA B:LEU501 4.6 24.1 1.0 CB B:TYR502 4.7 25.5 1.0 C21 B:4Y5602 4.8 21.5 1.0 CA B:LEU505 4.8 30.8 1.0 N B:LEU505 4.9 30.4 1.0 O1 B:4Y5602 5.0 25.0 1.0

Fluorine binding site 9 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:20.9 occ:1.00 F B:4Y5602 0.0 20.9 1.0 C5 B:4Y5602 1.3 21.2 1.0 C B:4Y5602 2.4 23.0 1.0 C4 B:4Y5602 2.4 22.8 1.0 F4 B:4Y5602 2.8 22.8 1.0 C16 B:4Y5602 3.1 18.8 1.0 C6 B:4Y5602 3.2 20.5 1.0 C15 B:4Y5602 3.3 18.7 1.0 CD2 B:LEU501 3.3 23.7 1.0 CG2 B:ILE328 3.4 19.8 1.0 CG B:LEU501 3.5 23.3 1.0 CD1 B:LEU501 3.7 22.2 1.0 C1 B:4Y5602 3.7 22.9 1.0 C3 B:4Y5602 3.7 21.5 1.0 C17 B:4Y5602 4.1 18.9 1.0 C2 B:4Y5602 4.2 23.2 1.0 CB B:ALA357 4.3 23.2 1.0 CG B:LEU505 4.3 29.4 1.0 N B:4Y5602 4.4 19.8 1.0 C20 B:4Y5602 4.4 19.6 1.0 CD2 B:LEU505 4.4 30.0 1.0 CD1 B:ILE328 4.5 22.2 1.0 O B:LEU353 4.6 21.5 1.0 N1 B:4Y5602 4.7 21.9 1.0 CB B:ILE328 4.7 20.3 1.0 CG1 B:ILE328 4.8 20.1 1.0 CG2 B:VAL332 4.9 19.6 1.0 CB B:LEU501 4.9 23.8 1.0 C18 B:4Y5602 5.0 18.7 1.0

Fluorine binding site 10 out of 12 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 5 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 5 Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:F602 b:26.8 occ:1.00 F1 B:4Y5602 0.0 26.8 1.0 C14 B:4Y5602 1.4 25.6 1.0 F3 B:4Y5602 2.2 29.8 1.0 F2 B:4Y5602 2.2 27.7 1.0 C9 B:4Y5602 2.4 25.9 1.0 C10 B:4Y5602 2.8 28.5 1.0 CB B:GLN487 3.5 26.2 1.0 CE2 B:PHE506 3.5 30.6 1.0 CG B:GLN487 3.6 24.9 1.0 C8 B:4Y5602 3.7 23.0 1.0 CD2 B:PHE506 3.7 28.8 1.0 CZ B:PHE506 3.8 28.8 1.0 O B:LEU505 3.9 35.9 1.0 CG B:GLN484 4.0 28.5 1.0 CA B:GLN484 4.1 23.8 1.0 CG B:PHE506 4.1 29.7 1.0 CE1 B:PHE506 4.1 28.8 1.0 C11 B:4Y5602 4.2 26.7 1.0 O B:LEU483 4.2 23.1 1.0 CD1 B:PHE506 4.3 27.5 1.0 C7 B:4Y5602 4.3 22.2 1.0 CD B:GLN487 4.4 24.8 1.0 N B:GLN484 4.4 23.6 1.0 C B:LEU483 4.5 23.7 1.0 CB B:GLN484 4.6 26.5 1.0 C B:LEU505 4.7 30.7 1.0 O B:4Y5602 4.8 25.2 1.0 OE1 B:GLN487 4.8 27.0 1.0 CA B:PHE506 4.8 33.8 1.0 C13 B:4Y5602 4.9 23.4 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