Fluorine in PDB 4i53: Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121

The structure of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121, PDB code: 4i53 was solved by M.Le-Khac, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.450, 127.670, 192.900, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 27.3

The structure of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 (pdb code 4i53). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121, PDB code: 4i53:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:53.2 occ:1.00 F23 A:1C1501 0.0 53.2 1.0 C22 A:1C1501 1.3 53.2 1.0 C21 A:1C1501 2.4 53.2 1.0 C24 A:1C1501 2.4 53.2 1.0 CL1 A:1C1501 2.9 53.2 1.0 OG A:SER375 3.0 8.9 1.0 O A:SER375 3.3 10.0 1.0 CE A:MET475 3.4 12.5 1.0 CA A:SER256 3.4 7.8 1.0 C20 A:1C1501 3.5 53.2 1.0 C A:SER256 3.7 8.3 1.0 C26 A:1C1501 3.7 53.2 1.0 CG2 A:THR257 3.7 8.4 1.0 C A:SER375 3.7 8.8 1.0 CG1 A:VAL255 3.7 4.9 1.0 N A:SER256 3.8 8.1 1.0 N A:THR257 3.9 7.8 1.0 CB A:SER375 4.0 9.0 1.0 O A:VAL255 4.1 3.9 1.0 C A:VAL255 4.1 4.5 1.0 C27 A:1C1501 4.1 53.2 1.0 N A:PHE376 4.1 23.0 1.0 O A:SER256 4.2 9.0 1.0 CA A:PHE376 4.3 21.5 1.0 CA A:SER375 4.4 9.2 1.0 CB A:THR257 4.7 8.3 1.0 N19 A:1C1501 4.7 53.2 1.0 SD A:MET475 4.7 13.2 1.0 O18 A:1C1501 4.7 53.2 1.0 CB A:SER256 4.8 7.5 1.0 OG1 A:THR257 4.8 7.7 1.0 CA A:THR257 4.9 8.3 1.0 CB A:VAL255 4.9 4.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Clade C1086 Hiv-1 GP120 Core in Complex with Dmj- II-121 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:53.2 occ:1.00 F23 B:1C1501 0.0 53.2 1.0 C22 B:1C1501 1.3 53.2 1.0 C21 B:1C1501 2.4 53.2 1.0 C24 B:1C1501 2.4 53.2 1.0 CL1 B:1C1501 2.9 53.2 1.0 OG B:SER375 3.2 13.4 1.0 CE B:MET475 3.3 24.9 1.0 CA B:SER256 3.4 28.2 1.0 O B:SER375 3.5 14.7 1.0 C20 B:1C1501 3.6 53.2 1.0 CG1 B:VAL255 3.6 22.5 1.0 C B:SER256 3.6 31.5 1.0 C26 B:1C1501 3.7 53.2 1.0 N B:SER256 3.7 28.7 1.0 CG2 B:THR257 3.7 17.9 1.0 C B:SER375 3.8 14.5 1.0 C B:VAL255 4.0 23.1 1.0 N B:THR257 4.0 18.8 1.0 O B:VAL255 4.0 17.1 1.0 C27 B:1C1501 4.1 53.2 1.0 CB B:SER375 4.1 13.8 1.0 O B:SER256 4.1 21.4 1.0 N B:PHE376 4.2 14.2 1.0 CA B:PHE376 4.4 14.1 1.0 CA B:SER375 4.6 14.8 1.0 SD B:MET475 4.6 25.9 1.0 N19 B:1C1501 4.7 53.2 1.0 CB B:THR257 4.7 18.1 1.0 O18 B:1C1501 4.7 53.2 1.0 CB B:SER256 4.8 28.6 1.0 CB B:VAL255 4.8 21.0 1.0 OG1 B:THR257 4.9 17.5 1.0 CA B:THR257 4.9 22.0 1.0 CA B:VAL255 5.0 23.6 1.0

J.M.Lalonde, M.Le-Khac, D.M.Jones, J.R.Courter, J.Park, A.Schon, A.M.Princiotto, X.Wu, J.R.Mascola, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Structure-Based Design and Synthesis of An Hiv-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. Acs Med Chem Lett V. 4 338 2013.
PubMed: 23667716
DOI: 10.1021/ML300407Y