Chlorine in PDB 6vke: Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein

The structure of Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein, PDB code: 6vke 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)	40.93 / 2.10
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	168.770, 168.770, 168.770, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.9

The binding sites of Chlorine atom in the Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein (pdb code 6vke). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein, PDB code: 6vke:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl602 b:21.8 occ:0.33 CL21 F:R0S602 0.0 21.8 0.3 C20 F:R0S602 1.8 26.5 0.3 C22 F:R0S602 2.7 26.9 0.3 C19 F:R0S602 2.8 26.9 0.3 O F:THR397 3.0 29.7 1.0 OD1 F:ASP486 3.5 55.8 1.0 CA F:ASP486 3.6 46.1 1.0 C F:ASP486 4.0 44.8 1.0 CB F:SER398 4.0 33.0 1.0 C23 F:R0S602 4.0 27.9 0.3 C F:THR397 4.1 29.0 1.0 C18 F:R0S602 4.1 28.2 0.3 N F:GLU487 4.1 42.5 1.0 O F:GLU487 4.2 33.7 1.0 N F:ASP486 4.3 44.3 1.0 C F:GLU487 4.4 34.4 1.0 CG F:ASP486 4.4 56.1 1.0 SD F:MET396 4.5 43.4 1.0 C24 F:R0S602 4.6 28.5 0.3 CA F:SER398 4.6 30.6 1.0 CB F:ASP486 4.6 52.1 1.0 N F:PHE488 4.7 30.9 1.0 O F:ASP486 4.7 45.0 1.0 N F:THR397 4.8 23.4 1.0 N F:SER398 4.8 26.4 1.0 CA F:PHE488 4.8 32.1 1.0 CB F:PHE488 4.9 35.1 1.0 CA F:GLU487 4.9 40.9 1.0 CB F:MET396 5.0 30.3 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl603 b:77.9 occ:1.00 NZ F:LYS315 3.1 25.8 1.0 NE1 F:TRP341 3.2 24.8 1.0 O F:HOH967 3.5 52.5 1.0 CE F:LYS315 3.9 23.8 1.0 CE2 F:TRP341 4.0 25.4 1.0 O F:HOH715 4.0 43.3 1.0 CG2 F:VAL360 4.1 36.6 1.0 CZ2 F:TRP341 4.1 26.6 1.0 CD F:LYS315 4.2 23.7 1.0 CD1 F:TRP341 4.3 22.1 1.0 O F:CYS358 4.5 35.0 1.0 O F:HOH787 5.0 33.0 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Inhibitor Jnj-40012665 in Complex with Prefusion Rsv F Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl604 b:69.3 occ:1.00 O F:HOH778 2.9 30.3 1.0 CB F:GLN462 3.3 51.4 1.0 N F:GLN462 3.4 40.5 1.0 O F:HOH762 3.7 37.2 1.0 CB F:ASN460 3.7 27.1 1.0 CA F:GLN462 3.8 46.3 1.0 N F:LYS461 4.0 28.7 1.0 CG F:ASN460 4.3 27.5 1.0 OD1 F:ASN460 4.3 29.6 1.0 C F:LYS461 4.3 36.3 1.0 CA F:ASN460 4.3 27.4 1.0 C F:ASN460 4.4 28.5 1.0 OE1 F:GLN462 4.6 67.1 1.0 CG F:GLN462 4.6 58.0 1.0 CA F:LYS461 4.8 32.1 1.0

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