Fluorine in PDB 4dko: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224, PDB code: 4dko was solved by Y.D.Kwon, J.M.Lalonde, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, J.Mascola, A.Schon, E.Freire, J.Sodroski, N.Madani, A.B.Smith Iii, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.94 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.723, 68.902, 94.515, 90.00, 91.23, 90.00
R / Rfree (%)	20.3 / 23.9

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 (pdb code 4dko). 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 A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224, PDB code: 4dko:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224


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 A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 within 5.0Å range: probe atom residue distance (Å) B Occ A:F513 b:46.7 occ:1.00 F25 A:0LM513 0.0 46.7 1.0 C03 A:0LM513 1.3 53.0 1.0 C02 A:0LM513 2.4 50.2 1.0 C04 A:0LM513 2.4 53.3 1.0 CL A:0LM513 2.9 64.6 1.0 OG A:SER375 3.0 30.2 1.0 CA A:SER256 3.3 15.9 1.0 C A:SER256 3.5 21.3 1.0 O A:SER375 3.5 22.1 1.0 CG2 A:THR257 3.6 21.9 1.0 C01 A:0LM513 3.6 47.8 1.0 C05 A:0LM513 3.6 64.5 1.0 N A:SER256 3.7 14.8 1.0 CG1 A:VAL255 3.7 18.0 1.0 N A:THR257 3.7 14.5 1.0 O A:VAL255 3.9 22.6 1.0 C A:VAL255 3.9 24.3 1.0 C A:SER375 3.9 24.1 1.0 O A:SER256 4.0 15.8 1.0 C06 A:0LM513 4.1 62.2 1.0 CB A:SER375 4.1 19.2 1.0 N A:PHE376 4.5 15.9 1.0 CB A:THR257 4.5 20.4 1.0 CD1 A:ILE475 4.5 29.4 1.0 OG1 A:THR257 4.5 20.3 1.0 CA A:PHE376 4.6 16.8 1.0 CA A:THR257 4.6 20.9 1.0 CA A:SER375 4.7 18.0 1.0 CB A:SER256 4.7 18.2 1.0 CB A:VAL255 4.7 15.5 1.0 N07 A:0LM513 4.8 67.1 1.0 O09 A:0LM513 4.8 61.0 1.0 CA A:VAL255 4.9 17.2 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224


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 A/E 93TH057 Hiv-1 GP120 Core in Complex with Ts-II-224 within 5.0Å range: probe atom residue distance (Å) B Occ C:F513 b:59.5 occ:1.00 F25 C:0LM513 0.0 59.5 1.0 C03 C:0LM513 1.3 51.9 1.0 C02 C:0LM513 2.3 49.7 1.0 C04 C:0LM513 2.4 54.3 1.0 CL C:0LM513 2.9 62.6 1.0 OG C:SER375 3.2 37.1 1.0 CA C:SER256 3.3 29.1 1.0 O C:SER375 3.3 26.6 1.0 O C:VAL255 3.5 34.0 1.0 N C:SER256 3.6 28.6 1.0 C C:SER256 3.6 30.5 1.0 C01 C:0LM513 3.6 55.8 1.0 C05 C:0LM513 3.6 72.6 1.0 CG1 C:VAL255 3.6 20.4 1.0 C C:VAL255 3.7 31.8 1.0 CG2 C:THR257 3.8 36.1 1.0 N C:THR257 3.9 29.2 1.0 C C:SER375 3.9 30.9 1.0 C06 C:0LM513 4.1 72.5 1.0 O C:SER256 4.1 26.0 1.0 CB C:SER375 4.2 33.7 1.0 N C:PHE376 4.4 26.6 1.0 CA C:PHE376 4.5 35.9 1.0 CB C:VAL255 4.6 21.0 1.0 CD1 C:ILE475 4.6 39.7 1.0 CB C:SER256 4.6 31.9 1.0 CA C:SER375 4.6 28.4 1.0 CA C:VAL255 4.7 22.6 1.0 CB C:THR257 4.8 40.4 1.0 N07 C:0LM513 4.8 81.7 1.0 O09 C:0LM513 4.8 90.2 1.0 CA C:THR257 4.9 34.5 1.0 OG1 C:THR257 4.9 33.6 1.0

J.M.Lalonde, Y.D.Kwon, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, A.Schon, E.Freire, P.D.Kwong, J.R.Mascola, J.Sodroski, N.Madani, A.B.Smith. Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule Hiv-1 Entry Inhibitors. J.Med.Chem. V. 55 4382 2012.
ISSN: ISSN 0022-2623
PubMed: 22497421
DOI: 10.1021/JM300265J