Fluorine in PDB 8v17: Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole

The structure of Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole, PDB code: 8v17 was solved by D.C.Goldstone, L.J.Walsham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 1.50
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	90.902, 90.902, 56.468, 90, 90, 120
R / Rfree (%)	14.2 / 17.1

The binding sites of Fluorine atom in the Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole (pdb code 8v17). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole, PDB code: 8v17:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:30.3 occ:1.00 F23 A:Y4X301 0.0 30.3 1.0 C22 A:Y4X301 1.3 26.4 1.0 C21 A:Y4X301 2.3 26.9 1.0 C24 A:Y4X301 2.4 20.3 1.0 O A:HOH431 2.9 19.5 1.0 CE A:MET66 3.0 25.2 0.5 CB A:MET66 3.1 17.9 0.5 CG A:MET66 3.2 17.8 0.5 CB A:MET66 3.2 17.6 0.5 SD A:MET66 3.2 18.4 0.5 CG A:MET66 3.5 18.2 0.5 O A:LEU56 3.6 17.8 1.0 C25 A:Y4X301 3.6 24.6 1.0 C20 A:Y4X301 3.6 24.7 1.0 C09 A:Y4X301 3.7 32.2 1.0 SD A:MET66 4.0 21.7 0.5 C A:LEU56 4.1 16.6 1.0 C27 A:Y4X301 4.1 25.1 1.0 N10 A:Y4X301 4.1 29.7 1.0 CB A:LEU56 4.2 16.9 1.0 CA A:MET66 4.3 16.2 0.5 OD1 A:ASN57 4.3 27.4 1.0 CA A:MET66 4.3 16.2 0.5 O A:MET66 4.6 17.8 1.0 N A:ASN57 4.7 15.8 1.0 CA A:LEU56 4.7 15.6 1.0 CE A:LYS70 4.7 28.4 1.0 F26 A:Y4X301 4.7 29.4 1.0 C A:MET66 4.7 17.7 1.0 CA A:ASN57 4.8 15.9 1.0 C08 A:Y4X301 4.8 28.8 1.0 OE1 A:GLN63 4.8 20.6 1.0 C19 A:Y4X301 4.8 26.1 1.0 NE2 A:GLN63 4.8 17.7 1.0 N05 A:Y4X301 4.9 27.4 1.0 CE A:MET66 5.0 19.2 0.5

Fluorine binding site 2 out of 2 in the Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-Ca Disulfide Linked Hexamer with Inhibitor Bound - Exploration of A Benzothiazole within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:29.4 occ:1.00 F26 A:Y4X301 0.0 29.4 1.0 C25 A:Y4X301 1.4 24.6 1.0 C27 A:Y4X301 2.3 25.1 1.0 C24 A:Y4X301 2.4 20.3 1.0 N A:LYS70 3.1 16.9 1.0 CG A:LYS70 3.2 23.9 1.0 CD1 A:ILE73 3.2 19.7 1.0 CG A:LEU69 3.3 20.3 1.0 CA A:LYS70 3.4 18.3 1.0 C A:LEU69 3.5 18.2 1.0 C22 A:Y4X301 3.6 26.4 1.0 C20 A:Y4X301 3.6 24.7 1.0 CB A:LEU69 3.6 18.2 1.0 O A:MET66 3.7 17.8 1.0 CD2 A:LEU69 3.7 21.6 1.0 CB A:LYS70 3.9 20.1 1.0 O A:LEU69 3.9 18.4 1.0 C21 A:Y4X301 4.1 26.9 1.0 CA A:LEU69 4.2 16.3 1.0 CD1 A:LEU56 4.2 20.9 1.0 CG1 A:ILE73 4.5 17.5 1.0 CD A:LYS70 4.5 26.4 1.0 CD1 A:LEU69 4.6 22.3 1.0 CE A:LYS70 4.6 28.4 1.0 F23 A:Y4X301 4.7 30.3 1.0 C A:LYS70 4.8 20.5 1.0 C A:MET66 4.8 17.7 1.0 C19 A:Y4X301 4.8 26.1 1.0 C36 A:Y4X301 4.8 25.3 1.0 C35 A:Y4X301 4.9 29.5 1.0

S.Xu, S.Wang, Y.Zhou, N.Foley, L.Sun, L.Walsham, K.Tang, D.Shi, X.Shi, Z.Zhang, X.Jiang, S.Gao, X.Liu, C.Pannecouque, D.C.Goldstone, A.Dick, P.Zhan. "Pseudosubstrate Envelope"/Free Energy Perturbation-Guided Design and Mechanistic Investigations of Benzothiazole Hiv Capsid Modulators with High Ligand Efficiency. J.Med.Chem. V. 67 19057 2024.
ISSN: ISSN 0022-2623
PubMed: 39418501
DOI: 10.1021/ACS.JMEDCHEM.4C01544