Atomistry » Fluorine » PDB 6wkd-6x37 » 6wml
Atomistry »
  Fluorine »
    PDB 6wkd-6x37 »
      6wml »

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

Protein crystallography data

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

Fluorine Binding Sites:

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 6wml

Go back to Fluorine Binding Sites List in 6wml
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 6wml

Go back to Fluorine Binding Sites List in 6wml
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 6wml

Go back to Fluorine Binding Sites List in 6wml
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 6wml

Go back to Fluorine Binding Sites List in 6wml
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

Reference:

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
Page generated: Fri Aug 2 03:49:47 2024

Last articles

Cl in 4AGU
Cl in 4AHN
Cl in 4AH4
Cl in 4AGR
Cl in 4AGG
Cl in 4ACF
Cl in 4AGA
Cl in 4AF8
Cl in 4AC2
Cl in 4ADG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy