Fluorine in PDB 4dkp: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-50

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-50, PDB code: 4dkp 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)	33.71 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.666, 68.483, 94.747, 90.00, 91.60, 90.00
R / Rfree (%)	19.9 / 22.5

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-50 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-50 (pdb code 4dkp). 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-50, PDB code: 4dkp:
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-50


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-50 within 5.0Å range: probe atom residue distance (Å) B Occ A:F513 b:39.4 occ:1.00 F24 A:0LL513 0.0 39.4 1.0 C21 A:0LL513 1.3 39.5 1.0 C20 A:0LL513 2.3 43.8 1.0 C22 A:0LL513 2.4 37.4 1.0 CL A:0LL513 2.9 56.6 1.0 OG A:SER375 3.1 30.0 1.0 CA A:SER256 3.4 15.8 1.0 C A:SER256 3.5 18.3 1.0 O A:SER375 3.5 20.9 1.0 C19 A:0LL513 3.6 41.8 1.0 CG2 A:THR257 3.6 24.1 1.0 C15 A:0LL513 3.6 43.5 1.0 N A:SER256 3.7 17.9 1.0 N A:THR257 3.7 19.0 1.0 CG1 A:VAL255 3.7 17.6 1.0 O A:VAL255 3.8 20.1 1.0 C A:VAL255 3.9 20.0 1.0 O A:SER256 4.0 15.2 1.0 C A:SER375 4.0 24.5 1.0 C18 A:0LL513 4.1 42.8 1.0 CB A:SER375 4.1 20.6 1.0 CD1 A:ILE475 4.4 24.6 1.0 N A:PHE376 4.5 18.7 1.0 CB A:THR257 4.5 21.5 1.0 CA A:PHE376 4.6 17.7 1.0 OG1 A:THR257 4.7 19.9 1.0 CA A:SER375 4.7 18.3 1.0 CA A:THR257 4.7 20.9 1.0 O16 A:0LL513 4.7 45.2 1.0 CB A:VAL255 4.7 20.3 1.0 CB A:SER256 4.8 14.7 1.0 N14 A:0LL513 4.8 45.4 1.0 CA A:VAL255 4.9 15.5 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-50


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-50 within 5.0Å range: probe atom residue distance (Å) B Occ C:F513 b:52.2 occ:1.00 F24 C:0LL513 0.0 52.2 1.0 C21 C:0LL513 1.3 45.6 1.0 C20 C:0LL513 2.3 38.7 1.0 C22 C:0LL513 2.3 43.9 1.0 CL C:0LL513 2.9 45.4 1.0 O C:SER375 3.2 28.2 1.0 OG C:SER375 3.3 32.3 1.0 O C:VAL255 3.4 29.8 1.0 CA C:SER256 3.4 26.9 1.0 C19 C:0LL513 3.6 32.6 1.0 C15 C:0LL513 3.6 48.9 1.0 C C:VAL255 3.7 23.4 1.0 CG1 C:VAL255 3.7 24.5 1.0 N C:SER256 3.7 27.5 1.0 C C:SER375 3.8 28.4 1.0 C C:SER256 3.8 23.0 1.0 CG2 C:THR257 4.1 34.2 1.0 C18 C:0LL513 4.1 46.0 1.0 N C:THR257 4.1 28.0 1.0 CB C:SER375 4.2 27.7 1.0 N C:PHE376 4.2 26.2 1.0 CA C:PHE376 4.3 30.9 1.0 O C:SER256 4.3 28.9 1.0 CB C:VAL255 4.6 21.6 1.0 CA C:SER375 4.6 23.8 1.0 CB C:SER256 4.7 27.6 1.0 CA C:VAL255 4.7 22.7 1.0 O16 C:0LL513 4.7 55.9 1.0 CD1 C:ILE475 4.8 41.0 1.0 N14 C:0LL513 4.8 52.3 1.0 CB C:THR257 5.0 31.3 1.0 OG1 C:THR257 5.0 33.8 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