Fluorine in PDB 3kdd: Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265

All present enzymatic activity of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265, PDB code: 3kdd was solved by E.E.Chufan, Y.Kawasaki, E.Freire, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.30 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.408, 85.916, 46.438, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26.2

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265 (pdb code 3kdd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265, PDB code: 3kdd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265


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 Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265 within 5.0Å range: probe atom residue distance (Å) B Occ A:F100 b:30.2 occ:0.55 F1 A:JZQ100 0.0 30.2 0.6 C37 A:JZQ100 0.5 19.9 0.5 C36 A:JZQ100 1.0 19.1 0.5 C42 A:JZQ100 1.3 28.4 0.6 C38 A:JZQ100 1.8 19.1 0.5 C39 A:JZQ100 2.2 19.4 0.5 C32 A:JZQ100 2.2 19.3 0.5 C41 A:JZQ100 2.4 28.8 0.6 C45 A:JZQ100 2.4 28.5 0.6 C34 A:JZQ100 2.6 19.5 0.5 O2 A:JZQ100 2.8 26.5 0.6 C33 A:JZQ100 2.8 19.0 0.5 C21 A:JZQ100 3.2 23.9 0.6 C35 A:JZQ100 3.3 18.9 0.5 C31 A:JZQ100 3.3 18.7 0.5 C40 A:JZQ100 3.6 28.0 0.6 C46 A:JZQ100 3.6 28.8 0.6 CD1 A:ILE47 3.8 24.1 1.0 CB A:ASP30 3.9 23.7 0.5 N A:ASP30 3.9 23.4 0.5 N A:ASP30 4.0 23.5 0.5 O A:ASP30 4.0 23.5 0.5 O7 A:JZQ100 4.0 18.6 0.5 OD2 A:ASP30 4.0 24.3 0.5 O A:ASP30 4.1 23.4 0.5 C47 A:JZQ100 4.1 29.3 0.6 CB A:ILE47 4.1 23.3 1.0 CG2 A:ILE47 4.2 23.8 1.0 CG A:ASP30 4.3 23.9 0.5 CB A:ASP30 4.3 23.9 0.5 CA A:ASP30 4.3 23.6 0.5 N A:ASP29 4.4 21.1 1.0 N4 A:JZQ100 4.4 17.7 0.5 CA A:ASP30 4.4 23.6 0.5 C A:ASP30 4.5 23.8 0.5 C A:ASP30 4.5 23.8 0.5 CG1 A:ILE47 4.5 23.4 1.0 CD1 A:LEU76 4.5 21.1 1.0 C12 A:JZQ100 4.5 21.9 0.6 CB A:ALA28 4.7 20.9 1.0 F2 A:JZQ100 4.7 31.0 0.6 CA A:ALA28 4.8 20.5 1.0 C A:ALA28 5.0 20.6 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265


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 Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265 within 5.0Å range: probe atom residue distance (Å) B Occ A:F100 b:28.4 occ:0.45 F1 A:JZQ100 0.0 28.4 0.5 C37 A:JZQ100 0.4 18.6 0.6 C36 A:JZQ100 1.0 18.0 0.6 C42 A:JZQ100 1.3 27.1 0.5 C38 A:JZQ100 1.5 18.2 0.6 C32 A:JZQ100 2.0 18.6 0.6 C34 A:JZQ100 2.3 17.6 0.6 C39 A:JZQ100 2.3 18.0 0.6 C41 A:JZQ100 2.4 27.9 0.5 C45 A:JZQ100 2.4 26.9 0.5 C33 A:JZQ100 2.6 19.1 0.6 O2 A:JZQ100 2.8 25.4 0.5 C21 A:JZQ100 3.1 24.3 0.5 C31 A:JZQ100 3.3 17.7 0.6 C35 A:JZQ100 3.3 17.8 0.6 C46 A:JZQ100 3.6 27.4 0.5 C40 A:JZQ100 3.6 26.7 0.5 N B:ASP30 3.8 20.4 1.0 O7 A:JZQ100 3.9 17.4 0.6 OD2 B:ASP30 3.9 25.2 1.0 CB B:ASP30 3.9 20.8 1.0 O B:ASP30 3.9 19.9 1.0 CG2 B:ILE47 4.0 25.6 1.0 CB B:ILE47 4.1 25.8 1.0 C47 A:JZQ100 4.1 27.8 0.5 CD1 B:ILE47 4.1 26.0 1.0 CG2 B:VAL32 4.2 21.6 0.5 CA B:ASP30 4.2 20.4 1.0 N B:ASP29 4.3 20.6 1.0 C B:ASP30 4.3 19.6 1.0 CG B:ASP30 4.3 23.5 1.0 N4 A:JZQ100 4.3 18.8 0.6 CB B:ALA28 4.3 20.5 1.0 C12 A:JZQ100 4.6 23.4 0.5 CA B:ALA28 4.6 20.3 1.0 CG1 B:ILE47 4.7 26.4 1.0 F2 A:JZQ100 4.7 29.1 0.5 C B:ALA28 4.8 20.4 1.0 C B:ASP29 4.8 20.9 1.0 CD1 B:LEU76 4.9 22.1 1.0 CA B:ASP29 5.0 21.3 1.0 CB B:ASP29 5.0 21.5 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265 within 5.0Å range: probe atom residue distance (Å) B Occ A:F100 b:31.0 occ:0.55 F2 A:JZQ100 0.0 31.0 0.6 O7 A:JZQ100 1.3 18.6 0.5 C46 A:JZQ100 1.3 28.8 0.6 C35 A:JZQ100 1.5 18.9 0.5 C31 A:JZQ100 2.3 18.7 0.5 N4 A:JZQ100 2.3 17.7 0.5 C47 A:JZQ100 2.4 29.3 0.6 C45 A:JZQ100 2.4 28.5 0.6 O2 A:JZQ100 2.7 26.5 0.6 C39 A:JZQ100 3.0 19.4 0.5 O A:HOH126 3.2 33.5 1.0 C30 A:JZQ100 3.3 19.3 0.5 C27 A:JZQ100 3.3 18.2 0.6 C20 A:JZQ100 3.3 18.0 0.5 C26 A:JZQ100 3.4 19.6 0.6 C32 A:JZQ100 3.5 19.3 0.5 C21 A:JZQ100 3.6 23.9 0.6 O A:HOH108 3.6 24.8 1.0 C40 A:JZQ100 3.6 28.0 0.6 C42 A:JZQ100 3.6 28.4 0.6 C36 A:JZQ100 3.8 19.1 0.5 O A:GLY48 3.8 26.1 1.0 O A:GLY27 3.9 19.9 1.0 O B:HOH160 3.9 33.2 1.0 C17 A:JZQ100 4.0 18.2 0.5 N2 A:JZQ100 4.1 20.2 0.6 O4 A:JZQ100 4.1 16.5 0.5 C41 A:JZQ100 4.1 28.8 0.6 C18 A:JZQ100 4.1 18.3 0.5 C12 A:JZQ100 4.3 21.9 0.6 CG A:ASP29 4.3 24.8 1.0 OD2 A:ASP29 4.3 29.6 1.0 OD1 A:ASP29 4.4 25.5 1.0 C22 A:JZQ100 4.4 18.4 0.6 N A:ASP29 4.5 21.1 1.0 C25 A:JZQ100 4.6 18.9 0.6 C33 A:JZQ100 4.6 19.0 0.5 F1 A:JZQ100 4.7 30.2 0.6 CB A:ASP29 4.8 22.8 1.0 C29 A:JZQ100 4.8 16.8 0.5 O B:HOH114 4.9 43.8 1.0 O A:HOH112 4.9 22.8 1.0 NH2 B:ARG8 4.9 28.0 0.5 CA A:ALA28 4.9 20.5 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10265 within 5.0Å range: probe atom residue distance (Å) B Occ A:F100 b:29.1 occ:0.45 F2 A:JZQ100 0.0 29.1 0.5 C46 A:JZQ100 1.3 27.4 0.5 O7 A:JZQ100 1.5 17.4 0.6 C35 A:JZQ100 1.5 17.8 0.6 C31 A:JZQ100 2.2 17.7 0.6 N4 A:JZQ100 2.3 18.8 0.6 C45 A:JZQ100 2.4 26.9 0.5 C47 A:JZQ100 2.4 27.8 0.5 O A:HOH146 2.5 41.9 1.0 O2 A:JZQ100 2.7 25.4 0.5 C30 A:JZQ100 3.0 18.4 0.6 C39 A:JZQ100 3.0 18.0 0.6 C26 A:JZQ100 3.1 24.5 0.5 C27 A:JZQ100 3.1 24.6 0.5 C20 A:JZQ100 3.2 18.4 0.6 O B:HOH134 3.4 42.6 1.0 C32 A:JZQ100 3.4 18.6 0.6 O B:GLY48 3.5 26.6 1.0 C42 A:JZQ100 3.6 27.1 0.5 C40 A:JZQ100 3.6 26.7 0.5 O A:HOH105 3.7 22.2 1.0 O A:HOH153 3.7 28.6 1.0 C21 A:JZQ100 3.7 24.3 0.5 C36 A:JZQ100 3.8 18.0 0.6 O B:GLY27 3.8 20.6 1.0 C17 A:JZQ100 3.8 18.4 0.6 N2 A:JZQ100 3.8 22.2 0.5 C18 A:JZQ100 3.9 19.9 0.6 NH2 A:ARG8 4.0 24.6 0.5 O4 A:JZQ100 4.0 17.3 0.6 C12 A:JZQ100 4.0 23.4 0.5 C41 A:JZQ100 4.1 27.9 0.5 C25 A:JZQ100 4.2 25.1 0.5 C22 A:JZQ100 4.2 24.9 0.5 OD1 B:ASP29 4.4 24.7 1.0 C29 A:JZQ100 4.4 19.1 0.6 CG B:ASP29 4.5 24.0 1.0 N B:ASP29 4.5 20.6 1.0 C33 A:JZQ100 4.6 19.1 0.6 OD2 B:ASP29 4.7 26.7 1.0 C B:GLY48 4.7 27.2 1.0 F1 A:JZQ100 4.7 28.4 0.5 CA B:ALA28 4.8 20.3 1.0 O B:HOH119 4.9 27.3 1.0 O8 A:JZQ100 4.9 22.3 0.5 C15 A:JZQ100 4.9 23.5 0.5 C B:GLY27 5.0 19.9 1.0 CZ A:ARG8 5.0 26.2 0.5 C13 A:JZQ100 5.0 22.7 0.5

Y.Kawasaki, E.E.Chufan, V.Lafont, K.Hidaka, Y.Kiso, L.Mario Amzel, E.Freire. How Much Binding Affinity Can Be Gained By Filling A Cavity? Chem.Biol.Drug Des. V. 75 143 2010.
ISSN: ISSN 1747-0277
PubMed: 20028396
DOI: 10.1111/J.1747-0285.2009.00921.X