Fluorine in PDB 1w5y: 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: 1w5y 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)	30.00 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.158, 86.954, 47.218, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.8

The binding sites of Fluorine atom in the Hiv-1 Protease in Complex with Fluoro Substituted Diol-Based C2- Symmetric Inhibitor (pdb code 1w5y). 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: 1w5y:
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:F1100 b:32.2 occ:1.00 F49 A:BE61100 0.0 32.2 1.0 C11 A:BE61100 1.4 24.9 1.0 C12 A:BE61100 2.4 25.0 1.0 C10 A:BE61100 2.5 25.0 1.0 CZ B:ARG8 2.8 23.5 1.0 NH2 B:ARG8 3.0 22.6 1.0 NE B:ARG8 3.1 18.4 1.0 NH1 B:ARG8 3.2 21.7 1.0 O36 A:BE61100 3.5 11.5 1.0 O A:GLY27 3.7 8.8 1.0 C07 A:BE61100 3.7 19.4 1.0 CD B:ARG8 3.7 18.1 1.0 C09 A:BE61100 3.9 22.0 1.0 CD2 B:LEU23 3.9 21.9 1.0 OD1 A:ASP29 4.2 17.3 1.0 C35 A:BE61100 4.3 15.8 1.0 C08 A:BE61100 4.3 23.9 1.0 OD2 A:ASP29 4.3 20.4 1.0 O A:HOH2036 4.4 18.3 1.0 CG A:ASP29 4.6 17.2 1.0 CG B:ARG8 4.7 15.4 1.0 N28 A:BE61100 4.7 14.8 1.0 CG2 B:VAL82 4.7 19.2 1.0 C A:GLY27 4.8 10.8 1.0 C13 A:BE61100 4.9 18.7 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:F1100 b:36.9 occ:1.00 F50 A:BE61100 0.0 36.9 1.0 C03 A:BE61100 1.3 28.7 1.0 C02 A:BE61100 2.4 28.0 1.0 C04 A:BE61100 2.4 28.7 1.0 CZ A:ARG8 2.6 23.7 1.0 NE A:ARG8 2.9 20.8 1.0 NH1 A:ARG8 3.0 23.4 1.0 NH2 A:ARG8 3.0 24.5 1.0 CD A:ARG8 3.4 20.9 1.0 O46 A:BE61100 3.5 13.0 1.0 C05 A:BE61100 3.7 26.8 1.0 C01 A:BE61100 3.7 25.7 1.0 O B:GLY27 3.7 10.7 1.0 CD2 A:LEU23 3.9 22.9 1.0 OD1 B:ASP29 4.1 17.1 1.0 C06 A:BE61100 4.2 27.6 1.0 C45 A:BE61100 4.2 14.1 1.0 O B:HOH2020 4.3 16.8 1.0 CG A:ARG8 4.4 20.2 1.0 OD2 B:ASP29 4.4 19.9 1.0 CG B:ASP29 4.6 16.1 1.0 N21 A:BE61100 4.6 12.8 1.0 C B:GLY27 4.8 9.3 1.0 C23 A:BE61100 4.9 22.1 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:F1100 b:28.8 occ:1.00 F51 A:BE61100 0.0 28.8 1.0 C06 A:BE61100 1.5 27.6 1.0 C01 A:BE61100 2.6 25.7 1.0 C05 A:BE61100 2.6 26.8 1.0 C23 A:BE61100 3.1 22.1 1.0 N B:ILE50 3.4 18.4 1.0 O22 A:BE61100 3.4 20.8 1.0 CG A:PRO81 3.4 24.1 1.0 C B:GLY49 3.5 18.9 1.0 CA B:ILE50 3.8 22.3 1.0 C02 A:BE61100 3.9 28.0 1.0 O20 A:BE61100 3.9 15.5 1.0 CA B:GLY49 3.9 18.3 1.0 C04 A:BE61100 3.9 28.7 1.0 O B:GLY49 4.0 16.4 1.0 C19 A:BE61100 4.1 14.9 1.0 CD A:PRO81 4.1 23.0 1.0 CG1 A:VAL82 4.2 23.8 1.0 CB B:ILE50 4.3 22.4 1.0 C18 A:BE61100 4.4 16.9 1.0 C03 A:BE61100 4.4 28.7 1.0 CD1 A:ILE84 4.6 20.1 1.0 CG1 B:ILE50 4.6 28.3 1.0 O A:HOH2043 4.7 13.1 1.0 CB A:PRO81 4.7 23.8 1.0 O B:GLY48 4.7 15.8 1.0 N21 A:BE61100 4.7 12.8 1.0 N B:GLY49 5.0 18.2 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:F1100 b:23.6 occ:1.00 F52 A:BE61100 0.0 23.6 1.0 C08 A:BE61100 1.2 23.9 1.0 C07 A:BE61100 2.3 19.4 1.0 C09 A:BE61100 2.3 22.0 1.0 C13 A:BE61100 2.9 18.7 1.0 CD1 A:ILE50 3.1 27.4 1.0 O14 A:BE61100 3.2 17.6 1.0 CA A:GLY49 3.5 18.2 1.0 N A:ILE50 3.5 19.4 1.0 C A:GLY49 3.5 18.2 1.0 O27 A:BE61100 3.6 18.5 1.0 C12 A:BE61100 3.6 25.0 1.0 C10 A:BE61100 3.7 25.0 1.0 C26 A:BE61100 3.8 13.8 1.0 CD B:PRO81 4.0 14.5 1.0 CG B:PRO81 4.0 15.7 1.0 C15 A:BE61100 4.0 16.5 1.0 CG1 A:ILE50 4.1 25.0 1.0 C11 A:BE61100 4.1 24.9 1.0 O A:GLY49 4.2 16.7 1.0 CB B:PRO81 4.3 13.2 1.0 CA A:ILE50 4.4 21.5 1.0 CG2 B:VAL82 4.4 19.2 1.0 N28 A:BE61100 4.5 14.8 1.0 O A:HOH2043 4.5 13.1 1.0 CD1 B:ILE84 4.6 18.1 1.0 N A:GLY49 4.7 17.1 1.0 O A:GLY48 4.8 16.6 1.0 CB A:ILE50 4.8 21.6 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