Fluorine in PDB 4dkr: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169, PDB code: 4dkr 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)	33.74 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.443, 68.602, 94.542, 90.00, 91.38, 90.00
R / Rfree (%)	19 / 20.8

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169 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 Aws-I-169 (pdb code 4dkr). 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 Aws-I-169, PDB code: 4dkr:
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 Aws-I-169


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 Aws-I-169 within 5.0Å range: probe atom residue distance (Å) B Occ A:F513 b:33.0 occ:1.00 F08 A:0LJ513 0.0 33.0 1.0 C03 A:0LJ513 1.3 29.4 1.0 C02 A:0LJ513 2.3 33.3 1.0 C04 A:0LJ513 2.3 23.5 1.0 CL7 A:0LJ513 2.9 40.0 1.0 CA A:SER256 3.2 20.0 1.0 OG A:SER375 3.2 36.3 1.0 C A:SER256 3.3 19.5 1.0 N A:SER256 3.5 18.4 1.0 CG2 A:THR257 3.5 21.8 1.0 N A:THR257 3.6 19.8 1.0 CG1 A:VAL255 3.6 23.5 1.0 C01 A:0LJ513 3.6 35.3 1.0 C05 A:0LJ513 3.6 31.1 1.0 O A:SER256 3.7 20.3 1.0 O A:SER375 3.7 20.6 1.0 C A:VAL255 3.9 23.7 1.0 O A:VAL255 4.0 23.0 1.0 C06 A:0LJ513 4.1 35.6 1.0 CD1 A:ILE475 4.1 30.9 1.0 C A:SER375 4.2 24.5 1.0 CB A:SER375 4.3 24.7 1.0 CB A:THR257 4.5 20.4 1.0 CA A:THR257 4.5 19.3 1.0 CB A:SER256 4.7 21.6 1.0 OG1 A:THR257 4.7 21.9 1.0 CB A:VAL255 4.7 24.9 1.0 O11 A:0LJ513 4.7 31.2 1.0 N A:PHE376 4.8 18.1 1.0 CA A:VAL255 4.8 20.5 1.0 N09 A:0LJ513 4.8 28.1 1.0 CA A:PHE376 4.9 16.6 1.0 CA A:SER375 4.9 18.7 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 Aws-I-169


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 Aws-I-169 within 5.0Å range: probe atom residue distance (Å) B Occ C:F513 b:52.7 occ:1.00 F08 C:0LJ513 0.0 52.7 1.0 C03 C:0LJ513 1.3 39.5 1.0 C02 C:0LJ513 2.3 39.0 1.0 C04 C:0LJ513 2.3 34.0 1.0 OG C:SER375 2.8 43.5 1.0 CL7 C:0LJ513 2.9 52.2 1.0 O C:SER375 3.2 32.8 1.0 CA C:SER256 3.4 28.4 1.0 C C:SER256 3.6 26.0 1.0 C01 C:0LJ513 3.6 39.1 1.0 C05 C:0LJ513 3.6 46.0 1.0 CG2 C:THR257 3.6 36.7 1.0 C C:SER375 3.7 35.1 1.0 N C:THR257 3.8 31.6 1.0 N C:SER256 3.8 30.7 1.0 CB C:SER375 3.8 38.9 1.0 O C:VAL255 3.9 33.2 1.0 CG1 C:VAL255 3.9 24.0 1.0 C C:VAL255 4.0 30.7 1.0 C06 C:0LJ513 4.1 54.0 1.0 O C:SER256 4.2 31.6 1.0 N C:PHE376 4.3 26.1 1.0 CA C:SER375 4.4 33.5 1.0 CA C:PHE376 4.5 31.9 1.0 CB C:THR257 4.6 36.5 1.0 OG1 C:THR257 4.6 35.0 1.0 CB C:SER256 4.7 34.9 1.0 CD1 C:ILE475 4.7 51.2 1.0 CA C:THR257 4.7 36.8 1.0 O11 C:0LJ513 4.8 47.3 1.0 N09 C:0LJ513 4.9 47.4 1.0 CB C:VAL255 4.9 21.7 1.0 O C:HOH707 5.0 38.2 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