Fluorine in PDB 7tjp: Hiv-1 GP120 Complex with Cjf-II-195

The structure of Hiv-1 GP120 Complex with Cjf-II-195, PDB code: 7tjp 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)	48.74 / 2.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.21, 121.635, 194.967, 90, 90, 90
R / Rfree (%)	22.4 / 26.5

The structure of Hiv-1 GP120 Complex with Cjf-II-195 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Cjf-II-195 (pdb code 7tjp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Cjf-II-195, PDB code: 7tjp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


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-195 within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:36.0 occ:0.38 F11 A:I6M510 0.0 36.0 0.4 F11 A:I6M510 0.1 36.3 0.6 C10 A:I6M510 1.4 31.3 0.4 C10 A:I6M510 1.4 31.1 0.6 C12 A:I6M510 2.4 34.0 0.4 C08 A:I6M510 2.4 29.9 0.4 C08 A:I6M510 2.4 29.7 0.6 C12 A:I6M510 2.4 34.1 0.6 OG A:SER375 2.9 26.1 1.0 CL09 A:I6M510 3.0 31.5 0.6 CL09 A:I6M510 3.0 29.1 0.4 O A:SER375 3.2 41.1 1.0 CG2 A:THR257 3.3 35.0 1.0 CA A:SER256 3.3 28.0 1.0 CE A:MET475 3.4 23.8 1.0 C A:SER256 3.6 31.2 1.0 C A:SER375 3.6 28.4 1.0 C05 A:I6M510 3.6 35.8 0.4 C07 A:I6M510 3.6 30.1 0.4 C05 A:I6M510 3.7 36.2 0.6 C07 A:I6M510 3.7 30.0 0.6 N A:THR257 3.7 20.5 1.0 N A:SER256 3.8 25.8 1.0 CG1 A:VAL255 3.8 28.1 1.0 CB A:SER375 3.9 27.1 1.0 N A:PHE376 4.1 32.8 1.0 O A:VAL255 4.1 29.7 1.0 C06 A:I6M510 4.1 31.8 0.4 C A:VAL255 4.1 22.8 1.0 C06 A:I6M510 4.2 31.8 0.6 CA A:PHE376 4.3 26.0 1.0 O A:SER256 4.3 31.8 1.0 CA A:SER375 4.4 23.1 1.0 CB A:THR257 4.5 22.2 1.0 CB A:SER256 4.6 20.1 1.0 O13 A:I6M510 4.6 34.0 0.6 O13 A:I6M510 4.6 34.2 0.4 CA A:THR257 4.7 20.6 1.0 N04 A:I6M510 4.9 34.8 0.4 N04 A:I6M510 4.9 35.1 0.6 OG1 A:THR257 4.9 29.4 1.0 SD A:MET475 5.0 23.2 1.0 N A:SER375 5.0 29.0 1.0

Fluorine binding site 2 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


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-195 within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:36.3 occ:0.62 F11 A:I6M510 0.0 36.3 0.6 F11 A:I6M510 0.1 36.0 0.4 C10 A:I6M510 1.3 31.3 0.4 C10 A:I6M510 1.4 31.1 0.6 C12 A:I6M510 2.3 34.0 0.4 C08 A:I6M510 2.3 29.9 0.4 C12 A:I6M510 2.4 34.1 0.6 C08 A:I6M510 2.4 29.7 0.6 OG A:SER375 2.9 26.1 1.0 CL09 A:I6M510 3.0 31.5 0.6 CL09 A:I6M510 3.0 29.1 0.4 O A:SER375 3.2 41.1 1.0 CG2 A:THR257 3.3 35.0 1.0 CA A:SER256 3.4 28.0 1.0 CE A:MET475 3.4 23.8 1.0 C05 A:I6M510 3.6 35.8 0.4 C07 A:I6M510 3.6 30.1 0.4 C05 A:I6M510 3.6 36.2 0.6 C07 A:I6M510 3.6 30.0 0.6 C A:SER375 3.6 28.4 1.0 C A:SER256 3.6 31.2 1.0 N A:THR257 3.7 20.5 1.0 CG1 A:VAL255 3.8 28.1 1.0 N A:SER256 3.9 25.8 1.0 CB A:SER375 3.9 27.1 1.0 C06 A:I6M510 4.1 31.8 0.4 N A:PHE376 4.1 32.8 1.0 C06 A:I6M510 4.1 31.8 0.6 O A:VAL255 4.2 29.7 1.0 C A:VAL255 4.2 22.8 1.0 CA A:PHE376 4.3 26.0 1.0 O A:SER256 4.3 31.8 1.0 CA A:SER375 4.4 23.1 1.0 CB A:THR257 4.5 22.2 1.0 O13 A:I6M510 4.5 34.0 0.6 O13 A:I6M510 4.6 34.2 0.4 CB A:SER256 4.6 20.1 1.0 CA A:THR257 4.7 20.6 1.0 N04 A:I6M510 4.8 34.8 0.4 N04 A:I6M510 4.8 35.1 0.6 OG1 A:THR257 4.9 29.4 1.0 O A:GLU370 5.0 35.9 1.0 SD A:MET475 5.0 23.2 1.0

Fluorine binding site 3 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


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-195 within 5.0Å range: probe atom residue distance (Å) B Occ B:F509 b:42.5 occ:0.58 F11 B:I6M509 0.0 42.5 0.6 F11 B:I6M509 0.0 42.5 0.4 C10 B:I6M509 1.4 35.8 0.6 C10 B:I6M509 1.4 35.5 0.4 C08 B:I6M509 2.3 34.7 0.6 C08 B:I6M509 2.3 34.6 0.4 C12 B:I6M509 2.4 35.7 0.6 C12 B:I6M509 2.4 35.7 0.4 OG B:SER375 2.8 29.2 1.0 CL09 B:I6M509 2.9 32.1 0.6 CL09 B:I6M509 2.9 31.6 0.4 O B:SER375 3.1 41.5 1.0 CG2 B:THR257 3.4 36.5 1.0 CA B:SER256 3.4 38.1 1.0 C B:SER375 3.5 32.6 1.0 C07 B:I6M509 3.6 37.2 0.6 C07 B:I6M509 3.6 37.1 0.4 CE B:MET475 3.6 31.4 1.0 C05 B:I6M509 3.6 35.7 0.6 C05 B:I6M509 3.6 35.5 0.4 CB B:SER375 3.7 29.2 1.0 C B:SER256 3.8 29.7 1.0 N B:THR257 3.8 22.3 1.0 CG1 B:VAL255 3.9 39.0 1.0 N B:PHE376 3.9 28.5 1.0 N B:SER256 3.9 41.5 1.0 C06 B:I6M509 4.1 34.7 0.6 C06 B:I6M509 4.1 34.5 0.4 CA B:PHE376 4.1 31.0 1.0 O B:VAL255 4.1 40.3 1.0 C B:VAL255 4.2 43.6 1.0 CA B:SER375 4.2 30.5 1.0 O B:SER256 4.5 41.0 1.0 CB B:THR257 4.6 29.1 1.0 CB B:SER256 4.7 33.9 1.0 O13 B:I6M509 4.8 39.3 0.4 O13 B:I6M509 4.8 39.3 0.6 CA B:THR257 4.8 30.9 1.0 N04 B:I6M509 4.9 35.3 0.6 N04 B:I6M509 4.9 35.3 0.4 N B:SER375 4.9 32.1 1.0 OG1 B:THR257 5.0 28.3 1.0 O B:GLU370 5.0 34.6 1.0

Fluorine binding site 4 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


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-195 within 5.0Å range: probe atom residue distance (Å) B Occ B:F509 b:42.5 occ:0.43 F11 B:I6M509 0.0 42.5 0.4 F11 B:I6M509 0.0 42.5 0.6 C10 B:I6M509 1.3 35.8 0.6 C10 B:I6M509 1.4 35.5 0.4 C08 B:I6M509 2.3 34.7 0.6 C08 B:I6M509 2.4 34.6 0.4 C12 B:I6M509 2.4 35.7 0.6 C12 B:I6M509 2.4 35.7 0.4 OG B:SER375 2.8 29.2 1.0 CL09 B:I6M509 2.9 32.1 0.6 CL09 B:I6M509 2.9 31.6 0.4 O B:SER375 3.1 41.5 1.0 CG2 B:THR257 3.4 36.5 1.0 CA B:SER256 3.5 38.1 1.0 C B:SER375 3.5 32.6 1.0 C07 B:I6M509 3.6 37.2 0.6 C05 B:I6M509 3.6 35.7 0.6 C07 B:I6M509 3.6 37.1 0.4 C05 B:I6M509 3.6 35.5 0.4 CE B:MET475 3.6 31.4 1.0 CB B:SER375 3.7 29.2 1.0 C B:SER256 3.8 29.7 1.0 N B:THR257 3.8 22.3 1.0 CG1 B:VAL255 3.9 39.0 1.0 N B:PHE376 3.9 28.5 1.0 N B:SER256 4.0 41.5 1.0 C06 B:I6M509 4.1 34.7 0.6 C06 B:I6M509 4.1 34.5 0.4 CA B:PHE376 4.1 31.0 1.0 O B:VAL255 4.2 40.3 1.0 CA B:SER375 4.2 30.5 1.0 C B:VAL255 4.3 43.6 1.0 O B:SER256 4.5 41.0 1.0 CB B:THR257 4.6 29.1 1.0 CB B:SER256 4.7 33.9 1.0 O13 B:I6M509 4.8 39.3 0.4 O13 B:I6M509 4.8 39.3 0.6 CA B:THR257 4.8 30.9 1.0 N04 B:I6M509 4.9 35.3 0.6 N04 B:I6M509 4.9 35.3 0.4 N B:SER375 4.9 32.1 1.0 OG1 B:THR257 4.9 28.3 1.0 O B:GLU370 5.0 34.6 1.0

Fluorine binding site 5 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hiv-1 GP120 Complex with Cjf-II-195 within 5.0Å range: probe atom residue distance (Å) B Occ D:F509 b:35.7 occ:0.53 F11 D:I6M509 0.0 35.7 0.5 F11 D:I6M509 0.1 35.8 0.5 C10 D:I6M509 1.4 30.9 0.5 C10 D:I6M509 1.4 30.6 0.5 C08 D:I6M509 2.3 32.4 0.5 C08 D:I6M509 2.3 32.3 0.5 C12 D:I6M509 2.4 34.4 0.5 C12 D:I6M509 2.4 34.3 0.5 CL09 D:I6M509 2.9 40.9 0.5 CL09 D:I6M509 2.9 40.7 0.5 OG D:SER375 3.0 33.3 1.0 O D:SER375 3.1 35.3 1.0 CA D:SER256 3.5 30.8 1.0 CG2 D:THR257 3.5 27.5 1.0 C D:SER375 3.5 36.2 1.0 C07 D:I6M509 3.6 32.2 0.5 C07 D:I6M509 3.6 32.0 0.5 C05 D:I6M509 3.6 36.2 0.5 CE D:MET475 3.6 24.5 1.0 C05 D:I6M509 3.7 36.1 0.5 CG1 D:VAL255 3.8 33.2 1.0 CB D:SER375 3.8 33.1 1.0 C D:SER256 3.8 31.2 1.0 N D:SER256 3.9 31.2 1.0 N D:PHE376 3.9 34.7 1.0 N D:THR257 3.9 27.7 1.0 O D:VAL255 4.1 44.3 1.0 C06 D:I6M509 4.1 35.2 0.5 CA D:PHE376 4.1 36.0 1.0 C06 D:I6M509 4.1 35.2 0.5 C D:VAL255 4.2 34.1 1.0 CA D:SER375 4.3 37.3 1.0 O D:SER256 4.5 23.3 1.0 O13 D:I6M509 4.6 34.9 0.5 CB D:SER256 4.7 24.8 1.0 O13 D:I6M509 4.7 34.7 0.5 CB D:THR257 4.7 23.6 1.0 N04 D:I6M509 4.9 34.5 0.5 N04 D:I6M509 4.9 34.4 0.5 CA D:THR257 4.9 26.4 1.0 CB D:VAL255 5.0 19.5 1.0

Fluorine binding site 6 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hiv-1 GP120 Complex with Cjf-II-195 within 5.0Å range: probe atom residue distance (Å) B Occ D:F509 b:35.8 occ:0.47 F11 D:I6M509 0.0 35.8 0.5 F11 D:I6M509 0.1 35.7 0.5 C10 D:I6M509 1.3 30.9 0.5 C10 D:I6M509 1.4 30.6 0.5 C08 D:I6M509 2.3 32.4 0.5 C08 D:I6M509 2.3 32.3 0.5 C12 D:I6M509 2.4 34.4 0.5 C12 D:I6M509 2.4 34.3 0.5 CL09 D:I6M509 2.9 40.9 0.5 OG D:SER375 2.9 33.3 1.0 CL09 D:I6M509 2.9 40.7 0.5 O D:SER375 3.1 35.3 1.0 CG2 D:THR257 3.5 27.5 1.0 CA D:SER256 3.5 30.8 1.0 C D:SER375 3.5 36.2 1.0 C07 D:I6M509 3.6 32.2 0.5 C07 D:I6M509 3.6 32.0 0.5 C05 D:I6M509 3.6 36.2 0.5 C05 D:I6M509 3.6 36.1 0.5 CE D:MET475 3.7 24.5 1.0 CB D:SER375 3.7 33.1 1.0 C D:SER256 3.8 31.2 1.0 CG1 D:VAL255 3.8 33.2 1.0 N D:PHE376 3.9 34.7 1.0 N D:THR257 3.9 27.7 1.0 N D:SER256 4.0 31.2 1.0 C06 D:I6M509 4.1 35.2 0.5 C06 D:I6M509 4.1 35.2 0.5 CA D:PHE376 4.1 36.0 1.0 O D:VAL255 4.1 44.3 1.0 C D:VAL255 4.2 34.1 1.0 CA D:SER375 4.2 37.3 1.0 O D:SER256 4.6 23.3 1.0 O13 D:I6M509 4.6 34.9 0.5 O13 D:I6M509 4.6 34.7 0.5 CB D:SER256 4.7 24.8 1.0 CB D:THR257 4.7 23.6 1.0 N04 D:I6M509 4.9 34.5 0.5 N04 D:I6M509 4.9 34.4 0.5 CA D:THR257 4.9 26.4 1.0 N D:SER375 5.0 30.9 1.0

Fluorine binding site 7 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hiv-1 GP120 Complex with Cjf-II-195 within 5.0Å range: probe atom residue distance (Å) B Occ C:F509 b:34.4 occ:0.32 F11 C:I6M509 0.0 34.4 0.3 F11 C:I6M509 0.1 34.0 0.7 C10 C:I6M509 1.4 26.2 0.3 C10 C:I6M509 1.4 25.6 0.7 C08 C:I6M509 2.4 24.1 0.3 C12 C:I6M509 2.4 28.4 0.3 C12 C:I6M509 2.4 24.1 0.7 C08 C:I6M509 2.4 24.3 0.7 CL09 C:I6M509 2.9 33.1 0.3 CL09 C:I6M509 3.0 32.0 0.7 OG C:SER375 3.1 29.9 1.0 O C:SER375 3.2 29.3 1.0 CA C:SER256 3.2 22.8 1.0 CG2 C:THR257 3.4 17.1 1.0 CE C:MET475 3.4 22.8 1.0 C C:SER256 3.6 22.1 1.0 C05 C:I6M509 3.6 25.4 0.3 C05 C:I6M509 3.6 24.9 0.7 C07 C:I6M509 3.6 23.5 0.3 C C:SER375 3.7 26.1 1.0 N C:SER256 3.7 28.8 1.0 CG1 C:VAL255 3.7 34.9 1.0 C07 C:I6M509 3.7 23.5 0.7 N C:THR257 3.7 21.4 1.0 O C:VAL255 4.0 34.6 1.0 CB C:SER375 4.0 28.6 1.0 C C:VAL255 4.0 35.4 1.0 C06 C:I6M509 4.1 27.2 0.3 N C:PHE376 4.1 25.5 1.0 C06 C:I6M509 4.1 26.5 0.7 CA C:PHE376 4.2 27.8 1.0 O C:SER256 4.3 24.1 1.0 CA C:SER375 4.4 26.2 1.0 CB C:SER256 4.5 31.3 1.0 CB C:THR257 4.6 20.5 1.0 O13 C:I6M509 4.7 25.6 0.7 O13 C:I6M509 4.7 25.9 0.3 CA C:THR257 4.7 26.4 1.0 N04 C:I6M509 4.8 25.2 0.3 N04 C:I6M509 4.9 25.0 0.7 CB C:VAL255 4.9 29.0 1.0 SD C:MET475 4.9 25.8 1.0

Fluorine binding site 8 out of 8 in the Hiv-1 GP120 Complex with Cjf-II-195


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hiv-1 GP120 Complex with Cjf-II-195 within 5.0Å range: probe atom residue distance (Å) B Occ C:F509 b:34.0 occ:0.68 F11 C:I6M509 0.0 34.0 0.7 F11 C:I6M509 0.1 34.4 0.3 C10 C:I6M509 1.3 26.2 0.3 C10 C:I6M509 1.4 25.6 0.7 C08 C:I6M509 2.3 24.1 0.3 C12 C:I6M509 2.3 28.4 0.3 C08 C:I6M509 2.3 24.3 0.7 C12 C:I6M509 2.4 24.1 0.7 CL09 C:I6M509 2.9 33.1 0.3 CL09 C:I6M509 2.9 32.0 0.7 OG C:SER375 3.1 29.9 1.0 O C:SER375 3.2 29.3 1.0 CA C:SER256 3.3 22.8 1.0 CE C:MET475 3.4 22.8 1.0 CG2 C:THR257 3.5 17.1 1.0 C07 C:I6M509 3.5 23.5 0.3 C05 C:I6M509 3.5 25.4 0.3 C05 C:I6M509 3.6 24.9 0.7 C07 C:I6M509 3.6 23.5 0.7 CG1 C:VAL255 3.6 34.9 1.0 C C:SER256 3.6 22.1 1.0 C C:SER375 3.7 26.1 1.0 N C:SER256 3.7 28.8 1.0 N C:THR257 3.8 21.4 1.0 O C:VAL255 4.0 34.6 1.0 C06 C:I6M509 4.0 27.2 0.3 C C:VAL255 4.0 35.4 1.0 C06 C:I6M509 4.0 26.5 0.7 CB C:SER375 4.0 28.6 1.0 N C:PHE376 4.1 25.5 1.0 CA C:PHE376 4.2 27.8 1.0 O C:SER256 4.3 24.1 1.0 CA C:SER375 4.5 26.2 1.0 CB C:SER256 4.6 31.3 1.0 CB C:THR257 4.7 20.5 1.0 O13 C:I6M509 4.7 25.9 0.3 O13 C:I6M509 4.7 25.6 0.7 N04 C:I6M509 4.8 25.2 0.3 N04 C:I6M509 4.8 25.0 0.7 CA C:THR257 4.8 26.4 1.0 CB C:VAL255 4.8 29.0 1.0 SD C:MET475 4.9 25.8 1.0 CA C:VAL255 5.0 31.7 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