Fluorine in PDB 8fly: Hiv-1 GP120 Complex with Bnm-III-170

The structure of Hiv-1 GP120 Complex with Bnm-III-170, PDB code: 8fly 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)	48.73 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.79, 120.78, 194.9, 90, 90, 90
R / Rfree (%)	24.7 / 27.6

The structure of Hiv-1 GP120 Complex with Bnm-III-170 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Bnm-III-170 (pdb code 8fly). 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 Bnm-III-170, PDB code: 8fly:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:31.4 occ:1.00 F23 A:5VG507 0.0 31.4 1.0 C22 A:5VG507 1.3 28.3 1.0 C24 A:5VG507 2.3 25.1 1.0 C21 A:5VG507 2.4 27.5 1.0 CL25 A:5VG507 2.8 44.8 1.0 OG A:SER375 3.2 27.2 1.0 O A:SER375 3.2 24.4 1.0 CA A:SER256 3.4 23.8 1.0 CG1 A:VAL255 3.6 21.5 1.0 C26 A:5VG507 3.6 26.6 1.0 C20 A:5VG507 3.6 23.2 1.0 C A:SER375 3.7 23.6 1.0 C A:SER256 3.7 22.9 1.0 N A:SER256 3.8 26.3 1.0 CE A:MET475 3.9 20.7 1.0 N A:THR257 3.9 26.3 1.0 CG2 A:THR257 3.9 24.4 1.0 O A:VAL255 4.0 28.1 1.0 C A:VAL255 4.0 24.4 1.0 C27 A:5VG507 4.1 24.1 1.0 CB A:SER375 4.1 23.9 1.0 N A:PHE376 4.2 24.5 1.0 CA A:PHE376 4.3 23.3 1.0 O A:SER256 4.4 24.6 1.0 CA A:SER375 4.5 25.6 1.0 O18 A:5VG507 4.7 26.2 1.0 CB A:SER256 4.7 22.0 1.0 CB A:VAL255 4.8 23.6 1.0 N19 A:5VG507 4.8 24.4 1.0 CB A:THR257 4.9 23.7 1.0 CA A:VAL255 5.0 23.7 1.0 CA A:THR257 5.0 20.1 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:27.1 occ:1.00 F23 B:5VG507 0.0 27.1 1.0 C22 B:5VG507 1.4 23.8 1.0 C24 B:5VG507 2.3 23.8 1.0 C21 B:5VG507 2.4 28.0 1.0 CL25 B:5VG507 2.8 25.5 1.0 OG B:SER375 3.2 23.2 1.0 O B:SER375 3.2 26.8 1.0 CA B:SER256 3.4 27.0 1.0 CG1 B:VAL255 3.6 26.2 1.0 C26 B:5VG507 3.6 26.1 1.0 C20 B:5VG507 3.6 23.2 1.0 C B:SER375 3.7 27.6 1.0 C B:SER256 3.7 27.4 1.0 N B:SER256 3.8 25.2 1.0 CE B:MET475 3.9 27.5 1.0 N B:THR257 3.9 26.8 1.0 CG2 B:THR257 3.9 23.4 1.0 O B:VAL255 4.0 29.4 1.0 C B:VAL255 4.0 25.6 1.0 C27 B:5VG507 4.1 22.3 1.0 CB B:SER375 4.1 25.3 1.0 N B:PHE376 4.2 27.4 1.0 CA B:PHE376 4.3 28.7 1.0 O B:SER256 4.4 25.8 1.0 CA B:SER375 4.5 25.1 1.0 O18 B:5VG507 4.7 29.2 1.0 CB B:SER256 4.7 28.5 1.0 CB B:VAL255 4.8 25.9 1.0 N19 B:5VG507 4.8 26.1 1.0 CB B:THR257 4.9 23.0 1.0 CA B:VAL255 5.0 25.6 1.0 CA B:THR257 5.0 24.1 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ C:F507 b:26.3 occ:1.00 F23 C:5VG507 0.0 26.3 1.0 C22 C:5VG507 1.4 23.4 1.0 C24 C:5VG507 2.3 19.3 1.0 C21 C:5VG507 2.4 22.0 1.0 CL25 C:5VG507 2.8 25.2 1.0 OG C:SER375 3.2 23.7 1.0 O C:SER375 3.2 24.6 1.0 CA C:SER256 3.4 21.5 1.0 CG1 C:VAL255 3.6 24.2 1.0 C26 C:5VG507 3.6 23.1 1.0 C20 C:5VG507 3.6 21.1 1.0 C C:SER375 3.7 22.4 1.0 C C:SER256 3.7 21.9 1.0 N C:SER256 3.8 26.5 1.0 CE C:MET475 3.9 26.3 1.0 N C:THR257 3.9 17.5 1.0 CG2 C:THR257 3.9 20.4 1.0 O C:VAL255 4.0 27.9 1.0 C C:VAL255 4.0 25.7 1.0 C27 C:5VG507 4.1 23.3 1.0 CB C:SER375 4.1 22.3 1.0 N C:PHE376 4.2 25.0 1.0 CA C:PHE376 4.3 23.6 1.0 O C:SER256 4.4 22.7 1.0 CA C:SER375 4.5 25.8 1.0 O18 C:5VG507 4.7 24.0 1.0 CB C:SER256 4.7 22.0 1.0 CB C:VAL255 4.8 19.4 1.0 N19 C:5VG507 4.8 25.1 1.0 CB C:THR257 4.9 20.6 1.0 CA C:VAL255 5.0 21.8 1.0 CA C:THR257 5.0 20.9 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ D:F507 b:31.0 occ:1.00 F23 D:5VG507 0.0 31.0 1.0 C22 D:5VG507 1.4 27.0 1.0 C24 D:5VG507 2.3 26.7 1.0 C21 D:5VG507 2.4 31.9 1.0 CL25 D:5VG507 2.8 30.8 1.0 OG D:SER375 3.2 27.9 1.0 O D:SER375 3.2 26.0 1.0 CA D:SER256 3.4 27.9 1.0 CG1 D:VAL255 3.6 24.5 1.0 C26 D:5VG507 3.6 25.2 1.0 C20 D:5VG507 3.6 29.4 1.0 C D:SER375 3.7 26.6 1.0 C D:SER256 3.7 27.9 1.0 N D:SER256 3.8 27.1 1.0 CE D:MET475 3.9 25.6 1.0 N D:THR257 3.9 31.4 1.0 CG2 D:THR257 3.9 28.4 1.0 O D:VAL255 4.0 32.1 1.0 C D:VAL255 4.0 29.9 1.0 C27 D:5VG507 4.1 28.3 1.0 CB D:SER375 4.1 27.4 1.0 N D:PHE376 4.2 26.9 1.0 CA D:PHE376 4.3 28.6 1.0 O D:SER256 4.4 27.2 1.0 CA D:SER375 4.5 28.8 1.0 O18 D:5VG507 4.7 31.6 1.0 CB D:SER256 4.7 26.1 1.0 CB D:VAL255 4.8 24.6 1.0 N19 D:5VG507 4.8 24.3 1.0 CB D:THR257 4.9 28.4 1.0 CA D:VAL255 5.0 25.9 1.0 CA D:THR257 5.0 29.5 1.0

C.J.Fritschi, S.Anang, Z.Gong, M.Mohammadi, J.Richard, C.Bourassa, K.T.Severino, H.Richter, D.Yang, H.C.Chen, T.J.Chiu, M.S.Seaman, N.Madani, C.Abrams, A.Finzi, W.A.Hendrickson, J.G.Sodroski, A.B.Smith Iii. Indoline CD4-Mimetic Compounds Mediate Potent and Broad Hiv-1 Inhibition and Sensitization to Antibody-Dependent Cellular Cytotoxicity. Proc.Natl.Acad.Sci.Usa V. 120 73120 2023.
ISSN: ESSN 1091-6490
PubMed: 36961924
DOI: 10.1073/PNAS.2222073120