Fluorine in PDB 7np5: Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216

The structure of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216, PDB code: 7np5 was solved by G.J.M.Oerlemans, B.A.Somsen, R.M.J.M.De Vries, F.A.Meijer, L.Brunsveld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.70 / 1.55
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.223, 108.223, 98.797, 90, 90, 120
R / Rfree (%)	23.4 / 27

The structure of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 (pdb code 7np5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216, PDB code: 7np5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:31.5 occ:1.00 F1 A:UKB601 0.0 31.5 1.0 C15 A:UKB601 1.3 36.1 1.0 F2 A:UKB601 2.1 38.7 1.0 F3 A:UKB601 2.1 33.5 1.0 C14 A:UKB601 2.4 34.3 1.0 C8 A:UKB601 2.8 27.3 1.0 C9 A:UKB601 3.0 28.5 1.0 N1 A:UKB601 3.1 32.4 1.0 C7 A:UKB601 3.5 27.5 1.0 NE2 A:GLN484 3.5 37.6 1.0 C13 A:UKB601 3.5 32.2 1.0 O A:LEU505 3.6 33.7 1.0 CB A:LEU505 3.6 31.8 1.0 CD1 A:LEU505 3.6 32.0 1.0 CZ A:PHE506 3.8 35.3 1.0 O4 A:UKB601 3.8 30.6 1.0 CD A:GLN484 4.0 45.6 1.0 CG A:LEU505 4.0 29.8 1.0 CE2 A:PHE506 4.0 28.4 1.0 C16 A:UKB601 4.0 26.4 1.0 CE1 A:PHE506 4.1 37.5 1.0 C A:LEU505 4.2 31.3 1.0 C6 A:UKB601 4.2 25.9 1.0 C10 A:UKB601 4.3 28.7 1.0 OE1 A:GLN484 4.3 41.9 1.0 O A:HOH705 4.4 47.9 1.0 O3 A:UKB601 4.4 27.9 1.0 CA A:LEU505 4.4 28.1 1.0 CD2 A:PHE506 4.5 31.1 1.0 CD1 A:PHE506 4.6 35.3 1.0 C12 A:UKB601 4.7 33.5 1.0 CG A:PHE506 4.8 32.4 1.0 CG A:GLN484 4.8 37.8 1.0

Fluorine binding site 2 out of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:38.7 occ:1.00 F2 A:UKB601 0.0 38.7 1.0 C15 A:UKB601 1.3 36.1 1.0 F1 A:UKB601 2.1 31.5 1.0 F3 A:UKB601 2.1 33.5 1.0 C14 A:UKB601 2.3 34.3 1.0 C13 A:UKB601 2.7 32.2 1.0 O A:HOH705 3.3 47.9 1.0 OE1 A:GLN484 3.3 41.9 1.0 CD A:GLN484 3.5 45.6 1.0 C9 A:UKB601 3.7 28.5 1.0 CE1 A:PHE506 3.7 37.5 1.0 CB A:GLN487 3.7 36.4 1.0 NE2 A:GLN484 3.8 37.6 1.0 CG A:GLN487 3.8 32.5 1.0 C12 A:UKB601 4.1 33.5 1.0 O A:LEU505 4.1 33.7 1.0 CZ A:PHE506 4.1 35.3 1.0 O A:LEU483 4.1 33.8 1.0 CD1 A:PHE506 4.2 35.3 1.0 CA A:GLN484 4.2 31.8 1.0 C8 A:UKB601 4.3 27.3 1.0 CG A:GLN484 4.4 37.8 1.0 C A:LEU483 4.4 31.1 1.0 N A:GLN484 4.4 33.2 1.0 N1 A:UKB601 4.5 32.4 1.0 CD A:GLN487 4.7 29.0 1.0 C10 A:UKB601 4.7 28.7 1.0 CE2 A:PHE506 4.8 28.4 1.0 CB A:LEU483 4.8 30.6 1.0 CB A:GLN484 4.9 31.6 1.0 C11 A:UKB601 4.9 33.9 1.0 CG A:PHE506 4.9 32.4 1.0 O A:HOH717 4.9 44.2 1.0

Fluorine binding site 3 out of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:33.5 occ:1.00 F3 A:UKB601 0.0 33.5 1.0 C15 A:UKB601 1.3 36.1 1.0 F2 A:UKB601 2.1 38.7 1.0 F1 A:UKB601 2.1 31.5 1.0 C14 A:UKB601 2.4 34.3 1.0 N1 A:UKB601 2.9 32.4 1.0 C9 A:UKB601 3.2 28.5 1.0 C8 A:UKB601 3.3 27.3 1.0 C13 A:UKB601 3.3 32.2 1.0 CD A:GLN484 3.3 45.6 1.0 NE2 A:GLN484 3.5 37.6 1.0 CB A:LEU483 3.5 30.6 1.0 CG A:GLN484 3.6 37.8 1.0 N A:GLN484 3.7 33.2 1.0 C A:LEU483 3.8 31.1 1.0 OE1 A:GLN484 3.8 41.9 1.0 CA A:GLN484 4.0 31.8 1.0 O4 A:UKB601 4.0 30.6 1.0 O A:VAL480 4.0 35.5 1.0 O A:LEU483 4.1 33.8 1.0 CG1 A:VAL480 4.3 34.5 1.0 CA A:LEU483 4.3 29.9 1.0 CB A:GLN484 4.4 31.6 1.0 C10 A:UKB601 4.4 28.7 1.0 C7 A:UKB601 4.5 27.5 1.0 CD1 A:LEU483 4.5 33.3 1.0 C12 A:UKB601 4.5 33.5 1.0 CG A:LEU483 4.7 30.7 1.0 CD1 A:LEU505 4.7 32.0 1.0 C16 A:UKB601 4.8 26.4 1.0 O A:HOH705 4.8 47.9 1.0 C A:VAL480 4.9 34.3 1.0 O A:LEU505 4.9 33.7 1.0 C11 A:UKB601 5.0 33.9 1.0

Fluorine binding site 4 out of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:32.7 occ:1.00 F4 A:UKB601 0.0 32.7 1.0 C22 A:UKB601 1.3 30.6 1.0 C21 A:UKB601 2.3 30.0 1.0 C2 A:UKB601 2.4 26.8 1.0 O1 A:UKB601 2.6 32.4 1.0 C1 A:UKB601 2.9 27.8 1.0 CG2 A:THR325 3.0 28.4 0.5 NE2 A:GLN329 3.1 31.2 1.0 CG A:GLN329 3.4 27.8 1.0 CD A:GLN329 3.5 35.3 1.0 C5 A:UKB601 3.6 26.1 1.0 C3 A:UKB601 3.6 29.3 1.0 CG1 A:VAL494 3.7 34.0 1.0 O A:THR325 3.9 29.1 0.5 CB A:THR325 3.9 32.9 0.5 O A:THR325 3.9 29.3 0.5 O2 A:UKB601 4.1 31.5 1.0 C4 A:UKB601 4.1 28.9 1.0 CB A:THR325 4.2 33.7 0.5 CA A:THR325 4.4 28.5 0.5 C A:THR325 4.4 33.3 0.5 C A:THR325 4.5 33.2 0.5 CA A:THR325 4.5 28.4 0.5 CG2 A:THR325 4.5 34.8 0.5 OE1 A:GLN329 4.5 35.5 1.0 OG1 A:THR325 4.7 35.5 0.5 O A:GLN495 4.8 39.0 1.0 O3 A:UKB601 4.8 27.9 1.0 CB A:GLN329 4.8 27.0 1.0 OG1 A:THR325 4.9 28.2 0.5 CG2 A:ILE328 4.9 28.0 1.0 C6 A:UKB601 5.0 25.9 1.0

F.A.Meijer, A.O.W.M.Saris, R.G.Doveston, G.J.M.Oerlemans, R.M.J.M.De Vries, B.A.Somsen, A.Unger, B.Klebl, C.Ottmann, P.J.Cossar, L.Brunsveld. Structure-Activity Relationship Studies of Trisubstituted Isoxazoles As Selective Allosteric Ligands For the Retinoic-Acid-Receptor-Related Orphan Receptor Gamma T. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34008974
DOI: 10.1021/ACS.JMEDCHEM.1C00475