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

Protein crystallography data

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

Other elements in 8fb1:

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

Fluorine Binding Sites:

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 8fb1

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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 8fb1

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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 8fb1

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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 8fb1

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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 8fb1

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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 8fb1

Go back to Fluorine Binding Sites List in 8fb1
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 8fb1

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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 8fb1

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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 8fb1

Go back to Fluorine Binding Sites List in 8fb1
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 8fb1

Go back to Fluorine Binding Sites List in 8fb1
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

Reference:

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
Page generated: Fri Aug 2 18:41:51 2024

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