Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Hiv-1 GP120 Complex with Bnm-III-170, PDB code: 5f4p:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:87.8 occ:1.00 CL25 D:5VG507 0.0 87.8 1.0 C24 D:5VG507 1.7 72.4 1.0 C26 D:5VG507 2.7 76.2 1.0 C22 D:5VG507 2.7 74.5 1.0 F23 D:5VG507 3.0 76.2 1.0 C D:PHE376 3.3 58.4 1.0 CA D:PHE376 3.4 60.0 1.0 N D:ASN377 3.5 62.5 1.0 O D:VAL255 3.6 65.1 1.0 O D:PHE376 3.8 62.7 1.0 N D:PHE376 3.9 58.5 1.0 CD2 D:PHE382 3.9 50.7 1.0 CG1 D:VAL255 4.0 67.7 1.0 C27 D:5VG507 4.0 70.3 1.0 C21 D:5VG507 4.0 72.9 1.0 CE2 D:PHE382 4.1 60.5 1.0 CB D:ASN377 4.2 52.8 1.0 C D:SER375 4.2 59.4 1.0 CA D:ASN377 4.3 63.0 1.0 O D:SER375 4.3 59.3 1.0 CH2 D:TRP112 4.4 63.7 1.0 C D:VAL255 4.4 64.3 1.0 CB D:VAL255 4.5 67.5 1.0 C20 D:5VG507 4.5 69.0 1.0 CB D:PHE376 4.8 56.0 1.0 OG D:SER375 5.0 69.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl501 b:92.8 occ:1.00 CL25 A:5VG501 0.0 92.8 1.0 C24 A:5VG501 1.7 71.8 1.0 C26 A:5VG501 2.7 66.9 1.0 C22 A:5VG501 2.7 64.8 1.0 F23 A:5VG501 3.0 75.2 1.0 C A:PHE376 3.3 48.4 1.0 CA A:PHE376 3.4 50.6 1.0 O A:PHE376 3.5 50.7 1.0 N A:ASN377 3.6 55.6 1.0 N A:PHE376 3.8 43.8 1.0 CD2 A:PHE382 3.8 53.5 1.0 O A:VAL255 3.8 52.1 1.0 C27 A:5VG501 4.0 67.7 1.0 C21 A:5VG501 4.0 69.3 1.0 CB A:ASN377 4.1 54.7 1.0 CE2 A:PHE382 4.2 61.3 1.0 C A:SER375 4.2 42.6 1.0 CA A:ASN377 4.3 56.8 1.0 O A:SER375 4.3 38.7 1.0 CG1 A:VAL255 4.4 46.0 1.0 C20 A:5VG501 4.5 75.6 1.0 CH2 A:TRP112 4.5 58.1 1.0 C A:VAL255 4.7 47.6 1.0 CB A:PHE376 4.9 48.0 1.0 CB A:SER375 4.9 53.3 1.0 CG A:PHE382 4.9 57.7 1.0 CB A:VAL255 5.0 47.5 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