Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Hiv-1 GP120 Complex with Jp-III-048, PDB code: 5f4l:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl501 b:52.7 occ:1.00 CL25 A:5VE501 0.0 52.7 1.0 C24 A:5VE501 1.7 48.9 1.0 C26 A:5VE501 2.7 43.9 1.0 C22 A:5VE501 2.8 41.1 1.0 F23 A:5VE501 3.0 49.4 1.0 C A:PHE376 3.2 35.1 1.0 CA A:PHE376 3.4 31.7 1.0 N A:ASN377 3.5 42.3 1.0 O A:PHE376 3.6 34.5 1.0 CD2 A:PHE382 3.7 34.5 1.0 N A:PHE376 3.7 41.6 1.0 O A:VAL255 3.9 48.4 1.0 C27 A:5VE501 4.0 43.7 1.0 CE2 A:PHE382 4.0 39.1 1.0 C21 A:5VE501 4.1 41.5 1.0 CB A:ASN377 4.1 34.5 1.0 CG1 A:VAL255 4.2 40.1 1.0 CA A:ASN377 4.2 42.1 1.0 C A:SER375 4.3 42.3 1.0 CH2 A:TRP112 4.3 41.8 1.0 O A:SER375 4.5 37.9 1.0 C20 A:5VE501 4.6 52.7 1.0 C A:VAL255 4.7 40.9 1.0 CB A:PHE376 4.8 34.3 1.0 CB A:VAL255 4.9 38.7 1.0 CG A:PHE382 4.9 43.1 1.0 OG A:SER375 4.9 40.5 1.0 CB A:SER375 4.9 34.7 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl501 b:58.9 occ:1.00 CL25 B:5VE501 0.0 58.9 1.0 C24 B:5VE501 1.7 46.8 1.0 C26 B:5VE501 2.7 54.0 1.0 C22 B:5VE501 2.8 55.6 1.0 F23 B:5VE501 3.0 64.0 1.0 C B:PHE376 3.2 44.0 1.0 CA B:PHE376 3.4 40.3 1.0 N B:ASN377 3.5 48.3 1.0 O B:PHE376 3.6 44.3 1.0 CD2 B:PHE382 3.7 42.2 1.0 N B:PHE376 3.8 44.6 1.0 O B:VAL255 3.9 55.2 1.0 CE2 B:PHE382 4.0 46.6 1.0 C27 B:5VE501 4.0 47.1 1.0 CB B:ASN377 4.0 44.1 1.0 C21 B:5VE501 4.1 53.2 1.0 CG1 B:VAL255 4.1 54.8 1.0 CA B:ASN377 4.2 44.5 1.0 C B:SER375 4.3 48.1 1.0 CH2 B:TRP112 4.3 50.9 1.0 O B:SER375 4.5 47.0 1.0 C20 B:5VE501 4.6 49.9 1.0 C B:VAL255 4.7 51.4 1.0 CB B:VAL255 4.8 50.9 1.0 CB B:PHE376 4.8 42.0 1.0 CG B:PHE382 4.9 39.1 1.0 OG B:SER375 4.9 50.4 1.0 CB B:SER375 5.0 47.4 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