Fluorine in PDB 5f4r: Hiv-1 GP120 Complex with Bnw-IV-147

The structure of Hiv-1 GP120 Complex with Bnw-IV-147, PDB code: 5f4r 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)	48.02 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.679, 127.357, 192.064, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 29.7

The structure of Hiv-1 GP120 Complex with Bnw-IV-147 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Bnw-IV-147 (pdb code 5f4r). 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 Bnw-IV-147, PDB code: 5f4r:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-1 GP120 Complex with Bnw-IV-147


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 Bnw-IV-147 within 5.0Å range: probe atom residue distance (Å) B Occ A:F508 b:88.2 occ:1.00 FAC A:5VF508 0.0 88.2 1.0 CAB A:5VF508 1.4 79.9 1.0 CAA A:5VF508 2.4 90.5 1.0 O A:SER375 2.4 45.5 1.0 CAD A:5VF508 2.4 83.9 1.0 OG A:SER375 2.5 48.3 1.0 C A:SER375 2.8 46.7 1.0 CLAE A:5VF508 3.0 0.4 1.0 CB A:SER375 3.1 44.8 1.0 N A:PHE376 3.4 43.9 1.0 CA A:SER375 3.5 50.3 1.0 CA A:SER256 3.6 50.0 1.0 CAH A:5VF508 3.7 79.8 1.0 CAF A:5VF508 3.7 84.6 1.0 CA A:PHE376 3.7 48.0 1.0 N A:THR257 3.7 51.7 1.0 CG2 A:THR257 3.8 51.1 1.0 C A:SER256 3.8 52.9 1.0 O A:VAL255 4.0 51.0 1.0 CE A:MET475 4.2 57.2 1.0 CAG A:5VF508 4.2 74.5 1.0 N A:SER256 4.2 45.5 1.0 OG1 A:THR257 4.2 50.3 1.0 N A:SER375 4.3 50.4 1.0 C A:VAL255 4.3 49.8 1.0 CG1 A:VAL255 4.4 54.1 1.0 CB A:THR257 4.5 52.8 1.0 O A:SER256 4.6 53.2 1.0 C A:PHE376 4.7 47.6 1.0 CA A:THR257 4.7 48.1 1.0 CB A:PHE376 4.8 50.5 1.0 CB A:SER256 4.8 48.9 1.0 OAK A:5VF508 4.9 83.3 1.0 NAI A:5VF508 4.9 79.8 1.0 O A:GLU370 4.9 51.0 1.0

Fluorine binding site 2 out of 2 in the Hiv-1 GP120 Complex with Bnw-IV-147


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 Bnw-IV-147 within 5.0Å range: probe atom residue distance (Å) B Occ C:F508 b:88.2 occ:1.00 FAC C:5VF508 0.0 88.2 1.0 CAB C:5VF508 1.4 79.9 1.0 O C:SER375 2.3 35.4 1.0 CAA C:5VF508 2.4 90.5 1.0 CAD C:5VF508 2.4 83.9 1.0 OG C:SER375 2.7 36.6 1.0 C C:SER375 2.8 38.4 1.0 CLAE C:5VF508 3.0 0.4 1.0 CB C:SER375 3.4 34.3 1.0 N C:PHE376 3.4 39.0 1.0 CA C:SER256 3.5 44.4 1.0 CA C:PHE376 3.7 43.7 1.0 CAH C:5VF508 3.7 79.8 1.0 CA C:SER375 3.7 37.8 1.0 CAF C:5VF508 3.7 84.6 1.0 C C:SER256 3.8 44.3 1.0 N C:THR257 3.8 43.3 1.0 CG2 C:THR257 4.0 41.3 1.0 O C:VAL255 4.0 54.5 1.0 N C:SER256 4.1 45.4 1.0 CAG C:5VF508 4.2 74.5 1.0 CE C:MET475 4.2 46.7 1.0 C C:VAL255 4.3 46.5 1.0 OG1 C:THR257 4.4 40.2 1.0 CG1 C:VAL255 4.4 45.0 1.0 N C:SER375 4.4 40.1 1.0 O C:SER256 4.6 45.4 1.0 C C:PHE376 4.6 44.4 1.0 CB C:THR257 4.6 38.1 1.0 CB C:SER256 4.7 42.9 1.0 CB C:PHE376 4.7 34.1 1.0 CA C:THR257 4.8 39.1 1.0 OAK C:5VF508 4.9 83.3 1.0 NAI C:5VF508 4.9 79.8 1.0 O C:GLU370 5.0 40.5 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