Fluorine in PDB 5f4l: Hiv-1 GP120 Complex with Jp-III-048

The structure of Hiv-1 GP120 Complex with Jp-III-048, PDB code: 5f4l was solved by S.Liang, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.44 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.159, 127.806, 192.470, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 28.8

The structure of Hiv-1 GP120 Complex with Jp-III-048 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Jp-III-048 (pdb code 5f4l). 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-1 GP120 Complex with Jp-III-048, PDB code: 5f4l:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-1 GP120 Complex with Jp-III-048


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 Jp-III-048 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:49.4 occ:1.00 F23 A:5VE501 0.0 49.4 1.0 C22 A:5VE501 1.3 41.1 1.0 C21 A:5VE501 2.4 41.5 1.0 C24 A:5VE501 2.4 48.9 1.0 OG A:SER375 2.9 40.5 1.0 O A:SER375 3.0 37.9 1.0 CL25 A:5VE501 3.0 52.7 1.0 C A:SER375 3.4 42.3 1.0 CA A:SER256 3.4 40.2 1.0 C20 A:5VE501 3.6 52.7 1.0 C26 A:5VE501 3.6 43.9 1.0 C A:SER256 3.7 37.7 1.0 CB A:SER375 3.7 34.7 1.0 N A:THR257 3.8 40.0 1.0 N A:PHE376 3.8 41.6 1.0 N A:SER256 3.9 39.8 1.0 CE A:MET475 3.9 31.8 1.0 CG2 A:THR257 3.9 37.0 1.0 O A:VAL255 4.0 48.4 1.0 CA A:PHE376 4.0 31.7 1.0 CG1 A:VAL255 4.1 40.1 1.0 C27 A:5VE501 4.1 43.7 1.0 C A:VAL255 4.1 40.9 1.0 CA A:SER375 4.1 35.2 1.0 OG1 A:THR257 4.3 42.0 1.0 O A:SER256 4.3 44.5 1.0 CB A:THR257 4.6 41.8 1.0 CB A:SER256 4.7 33.2 1.0 CA A:THR257 4.8 39.6 1.0 O18 A:5VE501 4.8 46.9 1.0 N19 A:5VE501 4.8 51.8 1.0 C A:PHE376 4.9 35.1 1.0 N A:SER375 4.9 35.2 1.0

Fluorine binding site 2 out of 2 in the Hiv-1 GP120 Complex with Jp-III-048


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 Jp-III-048 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:64.0 occ:1.00 F23 B:5VE501 0.0 64.0 1.0 C22 B:5VE501 1.3 55.6 1.0 C21 B:5VE501 2.4 53.2 1.0 C24 B:5VE501 2.4 46.8 1.0 OG B:SER375 2.6 50.4 1.0 O B:SER375 2.8 47.0 1.0 CL25 B:5VE501 3.0 58.9 1.0 C B:SER375 3.2 48.1 1.0 CB B:SER375 3.4 47.4 1.0 CA B:SER256 3.6 47.5 1.0 C20 B:5VE501 3.6 49.9 1.0 C26 B:5VE501 3.6 54.0 1.0 N B:PHE376 3.7 44.6 1.0 N B:THR257 3.8 46.8 1.0 C B:SER256 3.8 49.3 1.0 CA B:SER375 3.9 49.8 1.0 O B:VAL255 3.9 55.2 1.0 CA B:PHE376 3.9 40.3 1.0 N B:SER256 4.0 44.0 1.0 CG2 B:THR257 4.0 47.4 1.0 CG1 B:VAL255 4.1 54.8 1.0 C27 B:5VE501 4.1 47.1 1.0 CE B:MET475 4.1 47.2 1.0 C B:VAL255 4.2 51.4 1.0 OG1 B:THR257 4.4 48.5 1.0 O B:SER256 4.6 48.0 1.0 CB B:THR257 4.7 51.5 1.0 N B:SER375 4.7 52.0 1.0 CB B:SER256 4.8 50.3 1.0 C B:PHE376 4.8 44.0 1.0 N19 B:5VE501 4.8 52.9 1.0 O18 B:5VE501 4.8 49.8 1.0 CA B:THR257 4.9 45.9 1.0

B.Melillo, S.Liang, J.Park, A.Schon, J.R.Courter, J.M.Lalonde, D.J.Wendler, A.M.Princiotto, M.S.Seaman, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Small-Molecule CD4-Mimics: Structure-Based Optimization of Hiv-1 Entry Inhibition. Acs Med.Chem.Lett. V. 7 330 2016.
ISSN: ISSN 1948-5875
PubMed: 26985324
DOI: 10.1021/ACSMEDCHEMLETT.5B00471