Fluorine in PDB 6wml: Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod)

The structure of Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod), PDB code: 6wml was solved by T.C.Appleby, J.K.Perry, M.Mish, A.G.Villasenor, R.L.Mackman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.86 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.816, 141.575, 171.263, 90, 90.41, 90
R / Rfree (%)	21.1 / 25.5

The binding sites of Fluorine atom in the Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod) (pdb code 6wml). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod), PDB code: 6wml:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1017 b:52.6 occ:1.00 F21 A:U571017 0.0 52.6 1.0 C19 A:U571017 1.3 42.0 1.0 C18 A:U571017 2.4 34.3 1.0 C20 A:U571017 2.4 31.6 1.0 O B:HOH1204 3.3 46.8 1.0 CE2 B:TYR353 3.5 42.5 1.0 OH B:TYR353 3.6 51.4 1.0 CZ B:TYR353 3.6 45.9 1.0 N17 A:U571017 3.6 38.3 1.0 C01 A:U571017 3.6 38.2 1.0 CB B:PHE405 3.7 29.5 1.0 CG B:PHE405 3.9 35.4 1.0 CD1 B:PHE405 3.9 32.9 1.0 C02 A:U571017 4.1 36.1 1.0 O A:HOH1150 4.2 49.8 1.0 CD2 B:TYR353 4.3 44.7 1.0 CE1 B:TYR353 4.3 44.8 1.0 CD2 B:PHE405 4.7 29.3 1.0 N04 A:U571017 4.7 32.3 1.0 CE1 B:PHE405 4.8 32.1 1.0 O B:PHE405 4.8 44.0 1.0 CG B:TYR353 4.9 43.7 1.0 CD1 B:TYR353 4.9 46.5 1.0 CG B:ARG429 4.9 43.7 1.0

Fluorine binding site 2 out of 4 in the Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod) within 5.0Å range: probe atom residue distance (Å) B Occ B:F1018 b:49.1 occ:1.00 F21 B:U571018 0.0 49.1 1.0 C19 B:U571018 1.3 34.9 1.0 C18 B:U571018 2.4 35.6 1.0 C20 B:U571018 2.4 36.2 1.0 CE2 A:TYR353 3.5 41.1 1.0 OH A:TYR353 3.5 39.8 1.0 CZ A:TYR353 3.6 40.6 1.0 N17 B:U571018 3.6 40.0 1.0 C01 B:U571018 3.6 37.3 1.0 CB A:PHE405 3.8 39.9 1.0 CG A:PHE405 4.0 37.6 1.0 CD1 A:PHE405 4.1 36.2 1.0 C02 B:U571018 4.1 38.7 1.0 CD2 A:TYR353 4.2 30.4 1.0 CE1 A:TYR353 4.3 34.2 1.0 O B:HOH1138 4.4 45.8 1.0 N04 B:U571018 4.7 35.5 1.0 CD2 A:PHE405 4.8 32.2 1.0 O A:PHE405 4.8 44.5 1.0 CE1 A:PHE405 4.8 34.7 1.0 CG A:ARG429 4.9 45.5 1.0 CG A:TYR353 4.9 37.7 1.0 CD1 A:TYR353 5.0 41.7 1.0

Fluorine binding site 3 out of 4 in the Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod) within 5.0Å range: probe atom residue distance (Å) B Occ C:F917 b:60.9 occ:1.00 F21 C:U57917 0.0 60.9 1.0 C19 C:U57917 1.3 56.8 1.0 C18 C:U57917 2.4 52.7 1.0 C20 C:U57917 2.4 44.9 1.0 CZ D:TYR353 3.2 61.4 1.0 OH D:TYR353 3.2 62.1 1.0 CE2 D:TYR353 3.2 48.0 1.0 N17 C:U57917 3.6 45.0 1.0 C01 C:U57917 3.6 51.4 1.0 CB D:PHE405 3.9 43.7 1.0 CE1 D:TYR353 3.9 54.0 1.0 CD2 D:TYR353 4.0 58.9 1.0 C02 C:U57917 4.1 47.2 1.0 CG D:PHE405 4.1 50.6 1.0 CD1 D:PHE405 4.1 39.6 1.0 CD1 D:TYR353 4.6 59.2 1.0 CG D:TYR353 4.6 61.4 1.0 N04 C:U57917 4.7 49.8 1.0 O D:PHE405 4.7 47.8 1.0 CE D:LYS407 4.9 78.6 1.0 CG D:ARG429 4.9 51.2 1.0 CD2 D:PHE405 5.0 48.6 1.0

Fluorine binding site 4 out of 4 in the Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human TLR8 Bound to the Potent Agonist, Gs-9688 (Selgantolimod) within 5.0Å range: probe atom residue distance (Å) B Occ D:F918 b:49.6 occ:1.00 F21 D:U57918 0.0 49.6 1.0 C19 D:U57918 1.3 38.0 1.0 C18 D:U57918 2.4 37.8 1.0 C20 D:U57918 2.4 34.9 1.0 CE2 C:TYR353 3.4 41.7 1.0 OH C:TYR353 3.4 40.5 1.0 CZ C:TYR353 3.5 49.2 1.0 N17 D:U57918 3.6 36.7 1.0 C01 D:U57918 3.6 42.0 1.0 CB C:PHE405 3.9 35.1 1.0 CG C:PHE405 4.0 43.1 1.0 CD1 C:PHE405 4.1 39.2 1.0 C02 D:U57918 4.1 39.8 1.0 CD2 C:TYR353 4.1 44.0 1.0 CE1 C:TYR353 4.3 34.3 1.0 N04 D:U57918 4.7 44.1 1.0 O C:PHE405 4.8 45.4 1.0 CD2 C:PHE405 4.8 44.6 1.0 CG C:TYR353 4.9 43.7 1.0 CE1 C:PHE405 4.9 32.6 1.0 CG C:ARG429 4.9 50.7 1.0 CD1 C:TYR353 4.9 40.9 1.0

R.L.Mackman, M.Mish, G.Chin, J.K.Perry, T.Appleby, V.Aktoudianakis, S.Metobo, P.Pyun, C.Niu, S.Daffis, H.Yu, J.Zheng, A.G.Villasenor, J.Zablocki, J.Chamberlain, H.Jin, G.Lee, K.Suekawa-Pirrone, R.Santos, W.E.Delaney 4Th, S.P.Fletcher. Discovery of Gs-9688 (Selgantolimod) As A Potent and Selective Oral Toll-Like Receptor 8 Agonist For the Treatment of Chronic Hepatitis B. J.Med.Chem. V. 63 10188 2020.
ISSN: ISSN 0022-2623
PubMed: 32407112
DOI: 10.1021/ACS.JMEDCHEM.0C00100