Fluorine in PDB 1w5x: Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor

All present enzymatic activity of Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor:
3.4.23.16;

The structure of Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor, PDB code: 1w5x was solved by J.Lindberg, D.Pyring, S.Loewgren, A.Rosenquist, G.Zuccarello, I.Kvarnstroem, H.Zhang, L.Vrang, B.Claesson, A.Hallberg, B.Samuelsson, T.Unge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.79 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.460, 86.320, 46.570, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 21.6

The binding sites of Fluorine atom in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor (pdb code 1w5x). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor, PDB code: 1w5x:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:27.7 occ:1.00 F49 A:BE5501 0.0 27.7 1.0 C09 A:BE5501 1.5 21.7 1.0 C08 A:BE5501 2.6 23.0 1.0 C10 A:BE5501 2.6 24.4 1.0 F52 A:BE5501 3.0 24.3 1.0 CB B:PRO81 3.1 15.5 1.0 O A:GLY48 3.3 16.1 1.0 CG B:PRO81 3.3 18.1 1.0 O A:HOH2029 3.4 28.2 1.0 CA A:GLY49 3.6 18.3 1.0 C A:GLY48 3.8 16.8 1.0 C07 A:BE5501 3.9 21.0 1.0 C11 A:BE5501 3.9 23.6 1.0 N A:GLY49 4.0 16.9 1.0 C A:GLY49 4.0 17.5 1.0 O A:GLY49 4.2 16.3 1.0 CD B:PRO81 4.3 15.2 1.0 C12 A:BE5501 4.4 22.7 1.0 CA B:PRO81 4.6 15.7 1.0 O B:HOH2008 4.7 45.0 1.0 N A:ILE50 4.8 18.3 1.0 CA A:GLY48 4.9 15.2 1.0 O27 A:BE5501 4.9 20.1 1.0 C35 A:BE5501 5.0 16.8 1.0 C29 A:BE5501 5.0 16.0 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:29.6 occ:1.00 F50 A:BE5501 0.0 29.6 1.0 C05 A:BE5501 1.5 26.0 1.0 C06 A:BE5501 2.5 26.0 1.0 C04 A:BE5501 2.6 26.6 1.0 F51 A:BE5501 3.0 27.4 1.0 CG A:PRO81 3.0 26.0 1.0 O B:HOH2017 3.1 34.4 1.0 O B:GLY48 3.3 17.9 1.0 O B:GLY49 3.6 16.8 1.0 O B:HOH2038 3.6 33.6 1.0 O B:HOH2039 3.6 23.6 1.0 CB A:PRO81 3.6 23.6 1.0 C B:GLY49 3.7 18.2 1.0 C B:GLY48 3.8 18.6 1.0 CA B:GLY49 3.9 17.4 1.0 C03 A:BE5501 3.9 26.9 1.0 C01 A:BE5501 3.9 24.5 1.0 N B:GLY49 4.1 18.5 1.0 C02 A:BE5501 4.4 24.3 1.0 N B:ILE50 4.4 18.9 1.0 CD A:PRO81 4.4 23.5 1.0 CA B:GLY48 4.8 18.9 1.0 O A:HOH2009 4.9 43.1 1.0 CA B:ILE50 5.0 23.1 1.0 CA A:PRO81 5.0 22.8 1.0 CG1 A:VAL82 5.0 25.4 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:27.4 occ:1.00 F51 A:BE5501 0.0 27.4 1.0 C06 A:BE5501 1.5 26.0 1.0 C01 A:BE5501 2.6 24.5 1.0 C05 A:BE5501 2.6 26.0 1.0 F50 A:BE5501 3.0 29.6 1.0 C23 A:BE5501 3.1 23.0 1.0 O22 A:BE5501 3.1 22.0 1.0 N B:ILE50 3.1 18.9 1.0 C B:GLY49 3.4 18.2 1.0 CA B:ILE50 3.5 23.1 1.0 CG A:PRO81 3.6 26.0 1.0 O20 A:BE5501 3.6 18.2 1.0 CA B:GLY49 3.8 17.4 1.0 CB B:ILE50 3.9 24.9 1.0 C19 A:BE5501 3.9 17.4 1.0 C02 A:BE5501 3.9 24.3 1.0 C04 A:BE5501 3.9 26.6 1.0 O B:GLY49 4.0 16.8 1.0 C18 A:BE5501 4.1 18.9 1.0 O A:HOH2056 4.2 12.8 1.0 CD1 A:ILE84 4.3 19.8 1.0 CD A:PRO81 4.3 23.5 1.0 CG1 A:VAL82 4.3 25.4 1.0 C03 A:BE5501 4.4 26.9 1.0 CG1 B:ILE50 4.6 30.2 1.0 N21 A:BE5501 4.6 14.5 1.0 O B:GLY48 4.8 17.9 1.0 N B:GLY49 4.9 18.5 1.0 C B:ILE50 4.9 23.9 1.0 CB A:PRO81 5.0 23.6 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:24.3 occ:1.00 F52 A:BE5501 0.0 24.3 1.0 C08 A:BE5501 1.5 23.0 1.0 C07 A:BE5501 2.6 21.0 1.0 C09 A:BE5501 2.6 21.7 1.0 F49 A:BE5501 3.0 27.7 1.0 CD1 A:ILE50 3.0 29.1 1.0 O14 A:BE5501 3.0 19.3 1.0 C13 A:BE5501 3.1 21.1 1.0 N A:ILE50 3.2 18.3 1.0 CA A:GLY49 3.3 18.3 1.0 C A:GLY49 3.3 17.5 1.0 O27 A:BE5501 3.5 20.1 1.0 C26 A:BE5501 3.8 16.8 1.0 CG1 A:ILE50 3.8 23.2 1.0 CD B:PRO81 3.8 15.2 1.0 CG B:PRO81 3.9 18.1 1.0 C12 A:BE5501 3.9 22.7 1.0 C10 A:BE5501 4.0 24.4 1.0 CA A:ILE50 4.0 20.2 1.0 C15 A:BE5501 4.0 18.5 1.0 O A:GLY49 4.1 16.3 1.0 O A:HOH2056 4.2 12.8 1.0 CB B:PRO81 4.2 15.5 1.0 C11 A:BE5501 4.4 23.6 1.0 CD1 B:ILE84 4.5 21.5 1.0 CB A:ILE50 4.5 20.8 1.0 N A:GLY49 4.5 16.9 1.0 N28 A:BE5501 4.5 16.0 1.0 O A:GLY48 4.7 16.1 1.0 CG2 B:VAL82 4.7 19.0 1.0 N B:PRO81 5.0 15.0 1.0

J.Lindberg, D.Pyring, S.Loewgren, A.Rosenquist, G.Zuccarello, I.Kvarnstroem, H.Zhang, L.Vrang, B.Claesson, A.Hallberg, B.Samuelsson, T.Unge. Symmetric Fluoro-Substituted Diol-Based Hiv Protease Inhibitors. Ortho-Fluorinated and Meta-Fluorinated P1/P1'-Benzyloxy Side Groups Significantly Improve the Antiviral Activity and Preserve Binding Efficacy Eur.J.Biochem. V. 271 4594 2004.
ISSN: ISSN 0014-2956
PubMed: 15560801
DOI: 10.1111/J.1432-1033.2004.04431.X