Fluorine in PDB 5apk: Ligand Complex of Rorg Lbd

The structure of Ligand Complex of Rorg Lbd, PDB code: 5apk was solved by Y.Xue, A.Aagaard, F.Narjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.54 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.750, 99.750, 129.520, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.4

The structure of Ligand Complex of Rorg Lbd also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Ligand Complex of Rorg Lbd (pdb code 5apk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Ligand Complex of Rorg Lbd, PDB code: 5apk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ A:F1487 b:60.2 occ:1.00 F30 A:76E1487 0.0 60.2 1.0 C16 A:76E1487 1.3 65.3 1.0 C6 A:76E1487 2.3 68.3 1.0 C11 A:76E1487 2.4 66.1 1.0 C19 A:76E1487 2.8 61.8 1.0 CD1 A:ILE397 3.0 45.9 1.0 F33 A:76E1487 3.2 56.7 1.0 N25 A:76E1487 3.3 55.0 1.0 F32 A:76E1487 3.4 53.4 1.0 O26 A:76E1487 3.4 62.0 1.0 NE2 A:HIS479 3.5 89.2 1.0 C2 A:76E1487 3.6 68.8 1.0 C18 A:76E1487 3.6 70.0 1.0 CD1 A:ILE400 3.7 40.4 1.0 CD2 A:HIS479 3.8 89.5 1.0 C23 A:76E1487 3.9 52.9 1.0 CD2 A:LEU396 4.0 46.1 1.0 C8 A:76E1487 4.1 69.5 1.0 C14 A:76E1487 4.3 49.8 1.0 CG1 A:ILE397 4.3 39.9 1.0 F31 A:76E1487 4.4 53.1 1.0 CG A:LEU396 4.4 44.5 1.0 C4 A:76E1487 4.6 48.0 1.0 CE1 A:HIS479 4.8 89.0 1.0 CD1 A:LEU391 4.9 37.5 1.0

Fluorine binding site 2 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ A:F1487 b:53.1 occ:1.00 F31 A:76E1487 0.0 53.1 1.0 C23 A:76E1487 1.4 52.9 1.0 F33 A:76E1487 2.2 56.7 1.0 F32 A:76E1487 2.2 53.4 1.0 C13 A:76E1487 2.3 48.2 1.0 C3 A:76E1487 2.6 46.5 1.0 CD1 A:ILE397 3.5 45.9 1.0 C10 A:76E1487 3.6 45.5 1.0 CG2 A:ILE397 3.8 37.7 1.0 CE1 A:PHE401 3.8 34.6 1.0 CE2 A:PHE388 3.9 33.7 1.0 C1 A:76E1487 4.0 44.3 1.0 CD2 A:PHE388 4.0 32.0 1.0 CZ A:PHE388 4.1 33.3 1.0 CG A:PHE388 4.3 28.2 1.0 CE1 A:PHE388 4.4 33.4 1.0 F30 A:76E1487 4.4 60.2 1.0 CG1 A:ILE397 4.4 39.9 1.0 CG2 A:ILE400 4.4 33.5 1.0 CD1 A:PHE401 4.4 34.3 1.0 CD1 A:PHE388 4.5 30.7 1.0 CB A:ILE397 4.5 38.1 1.0 CD1 A:ILE400 4.7 40.4 1.0 C17 A:76E1487 4.7 47.9 1.0 O26 A:76E1487 4.7 62.0 1.0 CA A:ILE397 4.8 34.5 1.0 CB A:ILE400 4.8 34.7 1.0 CZ A:PHE401 4.8 32.7 1.0 C7 A:76E1487 4.9 43.6 1.0

Fluorine binding site 3 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ A:F1487 b:53.4 occ:1.00 F32 A:76E1487 0.0 53.4 1.0 C23 A:76E1487 1.4 52.9 1.0 F33 A:76E1487 2.2 56.7 1.0 F31 A:76E1487 2.2 53.1 1.0 C13 A:76E1487 2.4 48.2 1.0 O26 A:76E1487 2.7 62.0 1.0 C10 A:76E1487 2.9 45.5 1.0 C19 A:76E1487 3.3 61.8 1.0 F30 A:76E1487 3.4 60.2 1.0 CD1 A:ILE397 3.4 45.9 1.0 C3 A:76E1487 3.6 46.5 1.0 CD1 A:PHE388 3.6 30.7 1.0 CE1 A:PHE388 3.6 33.4 1.0 C16 A:76E1487 4.0 65.3 1.0 C11 A:76E1487 4.0 66.1 1.0 CG A:PHE388 4.0 28.2 1.0 CZ A:PHE388 4.1 33.3 1.0 N25 A:76E1487 4.2 55.0 1.0 C17 A:76E1487 4.2 47.9 1.0 C14 A:76E1487 4.4 49.8 1.0 CD2 A:PHE388 4.4 32.0 1.0 CE2 A:PHE388 4.4 33.7 1.0 SG A:CYS320 4.4 40.8 1.0 CG1 A:ILE397 4.6 39.9 1.0 CD1 A:LEU391 4.7 37.5 1.0 C9 A:76E1487 4.7 47.9 1.0 C1 A:76E1487 4.7 44.3 1.0 CB A:PHE388 4.8 25.9 1.0 C4 A:76E1487 4.8 48.0 1.0 O27 A:76E1487 5.0 54.1 1.0 C7 A:76E1487 5.0 43.6 1.0

Fluorine binding site 4 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ A:F1487 b:56.7 occ:1.00 F33 A:76E1487 0.0 56.7 1.0 C23 A:76E1487 1.4 52.9 1.0 F31 A:76E1487 2.2 53.1 1.0 F32 A:76E1487 2.2 53.4 1.0 C13 A:76E1487 2.4 48.2 1.0 C10 A:76E1487 3.1 45.5 1.0 F30 A:76E1487 3.2 60.2 1.0 C3 A:76E1487 3.3 46.5 1.0 C4 A:76E1487 3.3 48.0 1.0 C14 A:76E1487 3.4 49.8 1.0 O26 A:76E1487 3.4 62.0 1.0 C19 A:76E1487 3.5 61.8 1.0 CD1 A:ILE400 3.6 40.4 1.0 N25 A:76E1487 3.6 55.0 1.0 C5 A:76E1487 4.0 46.8 1.0 CD1 A:ILE397 4.0 45.9 1.0 CG2 A:ILE400 4.1 33.5 1.0 C9 A:76E1487 4.2 47.9 1.0 C16 A:76E1487 4.2 65.3 1.0 C17 A:76E1487 4.4 47.9 1.0 C11 A:76E1487 4.4 66.1 1.0 C1 A:76E1487 4.5 44.3 1.0 C15 A:76E1487 4.6 49.3 1.0 CB A:ILE400 4.7 34.7 1.0 CG1 A:ILE400 4.7 36.3 1.0 C12 A:76E1487 4.7 48.4 1.0 NE2 A:HIS479 4.7 89.2 1.0 C7 A:76E1487 4.9 43.6 1.0

Fluorine binding site 5 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ B:F1501 b:47.1 occ:1.00 F30 B:76E1501 0.0 47.1 1.0 C16 B:76E1501 1.3 51.4 1.0 C6 B:76E1501 2.3 53.4 1.0 C11 B:76E1501 2.4 54.0 1.0 C19 B:76E1501 2.8 50.7 1.0 N25 B:76E1501 3.0 49.5 1.0 CD1 B:ILE397 3.1 44.3 1.0 F33 B:76E1501 3.2 51.5 1.0 NE2 B:HIS479 3.3 60.0 1.0 CD2 B:HIS479 3.6 60.1 1.0 O26 B:76E1501 3.6 49.9 1.0 C18 B:76E1501 3.6 57.5 1.0 C2 B:76E1501 3.6 55.4 1.0 F32 B:76E1501 3.6 55.7 1.0 CD1 B:ILE400 3.6 41.0 1.0 CD2 B:LEU396 4.0 43.7 1.0 C23 B:76E1501 4.0 52.5 1.0 C14 B:76E1501 4.1 47.0 1.0 C8 B:76E1501 4.1 56.7 1.0 CG1 B:ILE397 4.4 35.7 1.0 C4 B:76E1501 4.4 44.8 1.0 CG B:LEU396 4.5 40.1 1.0 CE1 B:HIS479 4.5 59.8 1.0 F31 B:76E1501 4.6 53.5 1.0 CG B:HIS479 4.9 58.6 1.0

Fluorine binding site 6 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ B:F1501 b:53.5 occ:1.00 F31 B:76E1501 0.0 53.5 1.0 C23 B:76E1501 1.4 52.5 1.0 F32 B:76E1501 2.2 55.7 1.0 F33 B:76E1501 2.2 51.5 1.0 C13 B:76E1501 2.4 49.6 1.0 C3 B:76E1501 2.7 47.8 1.0 CD1 B:ILE397 3.6 44.3 1.0 C10 B:76E1501 3.7 48.0 1.0 CE1 B:PHE401 3.7 36.1 1.0 CG2 B:ILE397 3.9 32.0 1.0 CE2 B:PHE388 3.9 31.7 1.0 C1 B:76E1501 4.0 49.1 1.0 CD2 B:PHE388 4.1 31.5 1.0 CZ B:PHE388 4.1 31.9 1.0 CG2 B:ILE400 4.3 35.5 1.0 CD1 B:PHE401 4.3 36.2 1.0 CG B:PHE388 4.4 29.1 1.0 CE1 B:PHE388 4.4 33.4 1.0 CG1 B:ILE397 4.5 35.7 1.0 CD1 B:PHE388 4.6 30.4 1.0 CB B:ILE397 4.6 34.3 1.0 F30 B:76E1501 4.6 47.1 1.0 CD1 B:ILE400 4.7 41.0 1.0 C17 B:76E1501 4.7 51.6 1.0 CZ B:PHE401 4.8 36.9 1.0 CB B:ILE400 4.8 37.3 1.0 CE B:MET365 4.9 51.5 1.0 C7 B:76E1501 4.9 50.9 1.0 CA B:ILE397 4.9 32.4 1.0

Fluorine binding site 7 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ B:F1501 b:55.7 occ:1.00 F32 B:76E1501 0.0 55.7 1.0 C23 B:76E1501 1.4 52.5 1.0 F31 B:76E1501 2.2 53.5 1.0 F33 B:76E1501 2.2 51.5 1.0 C13 B:76E1501 2.4 49.6 1.0 C10 B:76E1501 2.9 48.0 1.0 O26 B:76E1501 3.2 49.9 1.0 CD1 B:ILE397 3.4 44.3 1.0 CD1 B:PHE388 3.5 30.4 1.0 C3 B:76E1501 3.5 47.8 1.0 CE1 B:PHE388 3.5 33.4 1.0 F30 B:76E1501 3.6 47.1 1.0 C19 B:76E1501 3.6 50.7 1.0 CG B:PHE388 3.9 29.1 1.0 CZ B:PHE388 3.9 31.9 1.0 CD2 B:PHE388 4.2 31.5 1.0 C16 B:76E1501 4.2 51.4 1.0 CE2 B:PHE388 4.3 31.7 1.0 N25 B:76E1501 4.3 49.5 1.0 C17 B:76E1501 4.3 51.6 1.0 C11 B:76E1501 4.3 54.0 1.0 C14 B:76E1501 4.5 47.0 1.0 CG1 B:ILE397 4.5 35.7 1.0 SG B:CYS320 4.6 41.9 1.0 C1 B:76E1501 4.7 49.1 1.0 CB B:PHE388 4.7 28.9 1.0 CD1 B:LEU391 4.7 38.8 1.0 C9 B:76E1501 4.8 46.0 1.0 C4 B:76E1501 4.9 44.8 1.0 CG2 B:ILE397 5.0 32.0 1.0 C7 B:76E1501 5.0 50.9 1.0

Fluorine binding site 8 out of 8 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ B:F1501 b:51.5 occ:1.00 F33 B:76E1501 0.0 51.5 1.0 C23 B:76E1501 1.4 52.5 1.0 F32 B:76E1501 2.2 55.7 1.0 F31 B:76E1501 2.2 53.5 1.0 C13 B:76E1501 2.4 49.6 1.0 C10 B:76E1501 3.1 48.0 1.0 F30 B:76E1501 3.2 47.1 1.0 C4 B:76E1501 3.3 44.8 1.0 C3 B:76E1501 3.3 47.8 1.0 C14 B:76E1501 3.4 47.0 1.0 N25 B:76E1501 3.5 49.5 1.0 C19 B:76E1501 3.6 50.7 1.0 CD1 B:ILE400 3.7 41.0 1.0 O26 B:76E1501 3.7 49.9 1.0 CD1 B:ILE397 4.0 44.3 1.0 C5 B:76E1501 4.0 45.6 1.0 C9 B:76E1501 4.1 46.0 1.0 CG2 B:ILE400 4.2 35.5 1.0 C16 B:76E1501 4.3 51.4 1.0 C17 B:76E1501 4.4 51.6 1.0 C11 B:76E1501 4.4 54.0 1.0 C1 B:76E1501 4.5 49.1 1.0 C15 B:76E1501 4.6 48.0 1.0 C12 B:76E1501 4.7 47.4 1.0 CB B:ILE400 4.7 37.3 1.0 CG1 B:ILE400 4.8 37.8 1.0 NE2 B:HIS479 4.8 60.0 1.0 SD B:MET365 4.9 54.7 1.0 CE B:MET365 5.0 51.5 1.0 C7 B:76E1501 5.0 50.9 1.0

R.I.Olsson, Y.Xue, S.Von Berg, A.Aagaard, J.Mcpheat, E.L.Hansson, J.Bernstrom, P.Hansson, J.Jirholt, H.Grindebacke, A.Leffler, R.Chen, Y.Xiong, H.Ge, T.G.Hansson, F.Narjes. Benzoxazepines Achieve Potent Suppression of Il-17 Release in Human T-Helper 17 (Th 17) Cells Through An Induced-Fit Binding Mode to the Nuclear Receptor Ror Gamma. Chemmedchem V. 11 207 2016.
ISSN: ESSN 1860-7187
PubMed: 26553345
DOI: 10.1002/CMDC.201500432