Fluorine in PDB 7tjo: Hiv-1 GP120 Complex with Cjf-II-197-S

The structure of Hiv-1 GP120 Complex with Cjf-II-197-S, PDB code: 7tjo was solved by Z.Gong, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.93 / 3.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.339, 121.826, 195.724, 90, 90, 90
R / Rfree (%)	22.9 / 26.8

The structure of Hiv-1 GP120 Complex with Cjf-II-197-S also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Cjf-II-197-S (pdb code 7tjo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Cjf-II-197-S, PDB code: 7tjo:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Cjf-II-197-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 GP120 Complex with Cjf-II-197-S within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:45.3 occ:1.00 F11 D:I6Q501 0.0 45.3 1.0 C10 D:I6Q501 1.4 39.9 1.0 C08 D:I6Q501 2.4 34.2 1.0 C12 D:I6Q501 2.4 45.8 1.0 CL09 D:I6Q501 2.9 57.1 1.0 OG D:SER375 3.2 44.3 1.0 O D:SER375 3.2 44.8 1.0 CE D:MET475 3.5 43.6 1.0 C D:SER375 3.6 37.8 1.0 CA D:SER256 3.6 36.9 1.0 CG1 D:VAL255 3.6 43.3 1.0 C07 D:I6Q501 3.6 28.8 1.0 C05 D:I6Q501 3.7 48.8 1.0 O D:VAL255 3.9 46.8 1.0 N D:SER256 3.9 38.4 1.0 CB D:SER375 3.9 37.9 1.0 CG2 D:THR257 3.9 42.6 1.0 C D:SER256 3.9 36.9 1.0 N D:PHE376 3.9 43.0 1.0 C D:VAL255 4.0 38.3 1.0 CA D:PHE376 4.0 45.3 1.0 C06 D:I6Q501 4.1 38.8 1.0 N D:THR257 4.1 34.9 1.0 CA D:SER375 4.3 38.1 1.0 O D:SER256 4.6 32.7 1.0 O13 D:I6Q501 4.7 49.2 1.0 CB D:SER256 4.8 37.7 1.0 CB D:VAL255 4.9 30.6 1.0 OG1 D:THR257 4.9 40.6 1.0 CB D:THR257 4.9 40.3 1.0 N04 D:I6Q501 4.9 47.7 1.0 C D:PHE376 5.0 45.8 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Cjf-II-197-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 GP120 Complex with Cjf-II-197-S within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:55.7 occ:1.00 F11 A:I6Q501 0.0 55.7 1.0 C10 A:I6Q501 1.4 41.7 1.0 C08 A:I6Q501 2.4 37.0 1.0 C12 A:I6Q501 2.4 40.3 1.0 CL09 A:I6Q501 2.9 51.8 1.0 OG A:SER375 3.2 32.3 1.0 O A:SER375 3.2 46.5 1.0 CE A:MET475 3.5 42.1 1.0 C A:SER375 3.6 43.9 1.0 CA A:SER256 3.6 35.2 1.0 CG1 A:VAL255 3.6 42.0 1.0 C07 A:I6Q501 3.7 40.7 1.0 C05 A:I6Q501 3.7 48.4 1.0 O A:VAL255 3.9 40.1 1.0 N A:SER256 3.9 37.6 1.0 CB A:SER375 3.9 29.6 1.0 CG2 A:THR257 3.9 38.1 1.0 C A:SER256 3.9 36.0 1.0 N A:PHE376 3.9 39.2 1.0 C A:VAL255 4.0 34.4 1.0 CA A:PHE376 4.0 40.5 1.0 C06 A:I6Q501 4.1 48.2 1.0 N A:THR257 4.1 28.7 1.0 CA A:SER375 4.3 32.3 1.0 O A:SER256 4.6 33.6 1.0 O13 A:I6Q501 4.7 45.9 1.0 CB A:SER256 4.8 36.4 1.0 CB A:VAL255 4.9 42.5 1.0 OG1 A:THR257 4.9 43.4 1.0 CB A:THR257 4.9 36.5 1.0 N04 A:I6Q501 4.9 48.4 1.0 C A:PHE376 5.0 47.4 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Cjf-II-197-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 GP120 Complex with Cjf-II-197-S within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:64.9 occ:1.00 F11 C:I6Q501 0.0 64.9 1.0 C10 C:I6Q501 1.4 33.8 1.0 C08 C:I6Q501 2.4 26.7 1.0 C12 C:I6Q501 2.4 30.9 1.0 CL09 C:I6Q501 2.9 96.4 1.0 OG C:SER375 3.2 30.6 1.0 O C:SER375 3.2 40.1 1.0 CE C:MET475 3.5 42.7 1.0 C C:SER375 3.6 36.2 1.0 CA C:SER256 3.6 30.6 1.0 CG1 C:VAL255 3.6 45.2 1.0 C07 C:I6Q501 3.7 29.3 1.0 C05 C:I6Q501 3.7 33.4 1.0 O C:VAL255 3.9 44.4 1.0 N C:SER256 3.9 38.6 1.0 CG2 C:THR257 3.9 32.4 1.0 CB C:SER375 3.9 32.1 1.0 C C:SER256 3.9 31.5 1.0 N C:PHE376 3.9 39.1 1.0 C C:VAL255 4.0 40.6 1.0 CA C:PHE376 4.0 43.7 1.0 C06 C:I6Q501 4.1 32.4 1.0 N C:THR257 4.1 34.2 1.0 CA C:SER375 4.3 35.8 1.0 O C:SER256 4.6 32.8 1.0 O13 C:I6Q501 4.7 28.3 1.0 CB C:SER256 4.8 34.9 1.0 CB C:VAL255 4.9 42.5 1.0 OG1 C:THR257 4.9 30.9 1.0 CB C:THR257 4.9 30.5 1.0 N04 C:I6Q501 4.9 39.8 1.0 C C:PHE376 5.0 45.0 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Cjf-II-197-S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 GP120 Complex with Cjf-II-197-S within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:53.7 occ:1.00 F11 B:I6Q501 0.0 53.7 1.0 C10 B:I6Q501 1.4 42.2 1.0 C08 B:I6Q501 2.4 35.4 1.0 C12 B:I6Q501 2.4 44.9 1.0 CL09 B:I6Q501 2.9 54.0 1.0 OG B:SER375 3.2 36.4 1.0 O B:SER375 3.2 54.8 1.0 CE B:MET475 3.5 43.7 1.0 C B:SER375 3.6 40.9 1.0 CA B:SER256 3.6 40.7 1.0 CG1 B:VAL255 3.6 48.8 1.0 C07 B:I6Q501 3.6 40.6 1.0 C05 B:I6Q501 3.7 47.9 1.0 O B:VAL255 3.9 42.5 1.0 N B:SER256 3.9 40.9 1.0 CB B:SER375 3.9 37.6 1.0 CG2 B:THR257 3.9 37.6 1.0 C B:SER256 3.9 34.3 1.0 N B:PHE376 3.9 39.7 1.0 C B:VAL255 4.0 46.0 1.0 CA B:PHE376 4.0 41.6 1.0 C06 B:I6Q501 4.1 47.8 1.0 N B:THR257 4.1 27.4 1.0 CA B:SER375 4.3 34.9 1.0 O B:SER256 4.6 34.6 1.0 O13 B:I6Q501 4.7 52.0 1.0 CB B:SER256 4.8 47.3 1.0 CB B:VAL255 4.9 44.3 1.0 OG1 B:THR257 4.9 39.9 1.0 CB B:THR257 4.9 37.9 1.0 N04 B:I6Q501 4.9 44.0 1.0 C B:PHE376 5.0 43.8 1.0

C.Chaplain, C.J.Fritschi, S.Anang, Z.Gong, J.Richard, C.Bourassa, S.Liang, M.Mohammadi, J.Park, A.Finzi, N.Madani, J.G.Sodroski, C.F.Abrams, W.A.Hendrickson, A.B.Smith. Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines Acs Medicinal Chemistry V. 14 51 2023LETTERS.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.2C00376