Fluorine in PDB 5f4p: Hiv-1 GP120 Complex with Bnm-III-170

The structure of Hiv-1 GP120 Complex with Bnm-III-170, PDB code: 5f4p 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)	48.24 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.378, 127.517, 192.945, 90.00, 90.00, 90.00
R / Rfree (%)	27.4 / 31.1

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

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Bnm-III-170 (pdb code 5f4p). 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 Bnm-III-170, PDB code: 5f4p:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 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 D:F507 b:76.2 occ:1.00 F23 D:5VG507 0.0 76.2 1.0 C22 D:5VG507 1.4 74.5 1.0 C21 D:5VG507 2.4 72.9 1.0 C24 D:5VG507 2.4 72.4 1.0 OG D:SER375 2.5 69.9 1.0 O D:SER375 2.6 59.3 1.0 CL25 D:5VG507 3.0 87.8 1.0 C D:SER375 3.0 59.4 1.0 CB D:SER375 3.2 63.9 1.0 N D:PHE376 3.6 58.5 1.0 C20 D:5VG507 3.7 69.0 1.0 C26 D:5VG507 3.7 76.2 1.0 CA D:SER375 3.7 66.8 1.0 CA D:SER256 3.7 65.8 1.0 CG2 D:THR257 3.8 66.6 1.0 N D:THR257 3.8 64.2 1.0 C D:SER256 3.9 65.5 1.0 CA D:PHE376 4.0 60.0 1.0 O D:VAL255 4.2 65.1 1.0 CE D:MET475 4.2 68.8 1.0 C27 D:5VG507 4.2 70.3 1.0 N D:SER256 4.2 67.1 1.0 OG1 D:THR257 4.3 59.2 1.0 C D:VAL255 4.4 64.3 1.0 N D:SER375 4.5 59.8 1.0 CB D:THR257 4.5 65.5 1.0 CG1 D:VAL255 4.5 67.7 1.0 O D:SER256 4.7 68.3 1.0 CA D:THR257 4.7 63.6 1.0 C D:PHE376 4.9 58.4 1.0 N19 D:5VG507 4.9 71.4 1.0 O18 D:5VG507 4.9 74.0 1.0 O D:GLU370 4.9 65.1 1.0 CB D:SER256 4.9 63.3 1.0

Fluorine binding site 2 out of 2 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 A:F501 b:75.2 occ:1.00 F23 A:5VG501 0.0 75.2 1.0 C22 A:5VG501 1.4 64.8 1.0 C21 A:5VG501 2.4 69.3 1.0 C24 A:5VG501 2.4 71.8 1.0 O A:SER375 2.5 38.7 1.0 OG A:SER375 2.7 56.3 1.0 C A:SER375 3.0 42.6 1.0 CL25 A:5VG501 3.0 92.8 1.0 CB A:SER375 3.3 53.3 1.0 N A:PHE376 3.6 43.8 1.0 C20 A:5VG501 3.7 75.6 1.0 C26 A:5VG501 3.7 66.9 1.0 CA A:SER256 3.7 51.3 1.0 CA A:SER375 3.7 46.0 1.0 CG2 A:THR257 3.8 57.9 1.0 N A:THR257 3.9 55.6 1.0 CA A:PHE376 3.9 50.6 1.0 C A:SER256 3.9 56.0 1.0 O A:VAL255 4.1 52.1 1.0 CE A:MET475 4.2 43.8 1.0 C27 A:5VG501 4.2 67.7 1.0 N A:SER256 4.3 45.8 1.0 OG1 A:THR257 4.3 58.2 1.0 C A:VAL255 4.4 47.6 1.0 N A:SER375 4.5 46.4 1.0 CB A:THR257 4.5 55.6 1.0 CG1 A:VAL255 4.6 46.0 1.0 O A:SER256 4.7 59.8 1.0 C A:PHE376 4.8 48.4 1.0 CA A:THR257 4.8 53.7 1.0 CB A:SER256 4.9 52.3 1.0 O18 A:5VG501 4.9 71.8 1.0 N19 A:5VG501 4.9 81.6 1.0 O A:GLU370 4.9 49.8 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