Fluorine in PDB 7ytx: Crystal Structure of TLR8 in Complex with Its Antagonist

The structure of Crystal Structure of TLR8 in Complex with Its Antagonist, PDB code: 7ytx was solved by T.Shimizu, K.Sakaniwa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.35 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.64, 97.57, 143.81, 90, 104.95, 90
R / Rfree (%)	22 / 29.6

The binding sites of Fluorine atom in the Crystal Structure of TLR8 in Complex with Its Antagonist (pdb code 7ytx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of TLR8 in Complex with Its Antagonist, PDB code: 7ytx:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of TLR8 in Complex with Its Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of TLR8 in Complex with Its Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:57.2 occ:1.00 F1 A:JRI901 0.0 57.2 1.0 C4 A:JRI901 1.4 59.1 1.0 C1 A:JRI901 2.4 57.2 1.0 C3 A:JRI901 2.5 60.2 1.0 N1 A:JRI901 2.9 59.1 1.0 N2 A:JRI901 3.0 63.0 1.0 C2 A:JRI901 3.0 59.1 1.0 CE2 A:PHE261 4.0 69.8 1.0 C9 A:JRI901 4.2 66.5 1.0 CZ A:PHE261 4.4 68.3 1.0 CE1 A:PHE346 4.5 56.7 1.0 CG2 A:ILE403 4.5 56.3 1.0 O1 A:JRI901 4.5 73.3 1.0 CZ A:PHE346 4.5 54.5 1.0 CG1 A:ILE403 4.6 54.8 1.0 OD1 A:ASN262 4.8 83.0 1.0 CD1 A:ILE403 5.0 55.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of TLR8 in Complex with Its Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of TLR8 in Complex with Its Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:52.1 occ:1.00 F1 B:JRI901 0.0 52.1 1.0 C4 B:JRI901 1.4 54.4 1.0 C1 B:JRI901 2.4 55.2 1.0 C3 B:JRI901 2.4 55.3 1.0 N2 B:JRI901 2.7 54.9 1.0 C2 B:JRI901 3.2 55.4 1.0 N1 B:JRI901 3.4 56.9 1.0 CE2 B:PHE261 3.9 66.1 1.0 CZ B:PHE261 4.0 64.2 1.0 C9 B:JRI901 4.0 55.3 1.0 OH A:TYR567 4.2 50.6 1.0 CZ A:TYR567 4.2 51.7 1.0 CE2 A:TYR567 4.3 52.9 1.0 O1 B:JRI901 4.5 57.7 1.0 CG2 B:ILE403 4.7 49.1 1.0 CD1 B:ILE403 4.8 49.4 1.0 CE1 A:TYR567 4.8 51.7 1.0 O2 B:JRI901 4.8 55.3 1.0 C5 B:JRI901 4.9 56.8 1.0

S.T.Ishizaka, L.Hawkins, Q.Chen, F.Tago, T.Yagi, K.Sakaniwa, Z.Zhang, T.Shimizu, M.Shirato. A Novel Toll-Like Receptor 7/8-Specific Antagonist E6742 Ameliorates Clinically Relevant Disease Parameters in Murine Models of Lupus. Eur.J.Pharmacol. V. 957 75962 2023.
ISSN: ISSN 0014-2999
PubMed: 37544422
DOI: 10.1016/J.EJPHAR.2023.175962