Fluorine in PDB 6vkc: Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein

The structure of Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein, PDB code: 6vkc was solved by J.S.Mclellan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 2.60
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	168.040, 168.040, 168.040, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.9

The structure of Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein (pdb code 6vkc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein, PDB code: 6vkc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein


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 Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:F610 b:57.5 occ:0.33 F01 F:R0J610 0.0 57.5 0.3 C02 F:R0J610 1.4 57.8 0.3 F04 F:R0J610 2.2 57.7 0.3 F03 F:R0J610 2.2 57.6 0.3 C05 F:R0J610 2.4 57.7 0.3 C06 F:R0J610 2.8 57.6 0.3 CZ F:PHE488 3.2 76.1 1.0 CD1 F:PHE137 3.7 56.9 1.0 CE1 F:PHE488 3.7 73.9 1.0 O2 F:TAR611 3.7 0.6 1.0 O F:PHE137 3.9 42.7 1.0 CE2 F:PHE488 4.1 76.0 1.0 CA F:PHE137 4.1 42.1 1.0 C07 F:R0J610 4.3 57.5 0.3 CB F:PHE137 4.4 44.8 1.0 C F:PHE137 4.5 43.2 1.0 CE1 F:PHE137 4.5 61.8 1.0 CG F:PHE137 4.5 52.3 1.0 O41 F:TAR611 4.9 0.9 1.0 CD1 F:PHE488 4.9 70.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein


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 Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:F610 b:57.6 occ:0.33 F03 F:R0J610 0.0 57.6 0.3 C02 F:R0J610 1.4 57.8 0.3 F01 F:R0J610 2.2 57.5 0.3 F04 F:R0J610 2.2 57.7 0.3 C05 F:R0J610 2.4 57.7 0.3 C06 F:R0J610 3.1 57.6 0.3 C07 F:R0J610 4.1 57.5 0.3 O2 F:TAR611 4.2 0.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Inhibitor Jnj-36811054 in Complex with Prefusion Rsv F Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:F610 b:57.7 occ:0.33 F04 F:R0J610 0.0 57.7 0.3 C02 F:R0J610 1.4 57.8 0.3 F01 F:R0J610 2.2 57.5 0.3 F03 F:R0J610 2.2 57.6 0.3 C05 F:R0J610 2.4 57.7 0.3 O2 F:TAR611 3.1 0.6 1.0 O41 F:TAR611 3.3 0.9 1.0 C06 F:R0J610 3.7 57.6 0.3 C15 F:R0J610 4.1 57.7 0.3 O F:PHE137 4.1 42.7 1.0 C4 F:TAR611 4.2 0.1 1.0 C2 F:TAR611 4.3 0.4 1.0 C3 F:TAR611 4.5 0.6 1.0 N14 F:R0J610 4.5 57.7 0.3 CZ F:PHE488 4.7 76.1 1.0 C F:PHE137 4.9 43.2 1.0 C07 F:R0J610 4.9 57.5 0.3 C16 F:R0J610 5.0 57.7 0.3 C12 F:R0J610 5.0 57.6 0.3

S.Vendeville, A.Tahri, L.Hu, S.Demin, L.Cooymans, A.Vos, L.Kwanten, J.Van Den Berg, M.Battles, J.Mclellan, A.Koul, P.Raboisson, D.Roymans, T.H.M.Jonckers. Discovery of 3 ({5 Chloro-1 [3 (Methylsulfonyl)Propyl]-1H Indol-2 Yl}Methyl)-1 (2,2,2 Trifluoroethyl)-1,3 Dihydro-2H Imidazo[4,5-C]Pyridin-2 One (Jnj-53718678), A Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32407115
DOI: 10.1021/ACS.JMEDCHEM.0C00226