Fluorine in PDB 6mkl: X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142

The structure of X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142, PDB code: 6mkl was solved by R.S.Yedidi, H.Hayashi, D.Das, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.85 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	63.284, 63.284, 82.072, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 18.8

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142 (pdb code 6mkl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142, PDB code: 6mkl:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:18.4 occ:0.50 F1 A:7OA400 0.0 18.4 0.5 C33 A:7OA400 1.3 15.5 0.5 C06 A:7OA400 2.4 13.4 0.5 C35 A:7OA400 2.4 14.9 0.5 O A:HOH572 2.7 40.3 1.0 C11 A:7OA400 3.1 16.4 0.5 C15 A:7OA400 3.2 11.6 0.5 NH2 A:ARG8 3.7 24.1 1.0 C07 A:7OA400 3.7 11.9 0.5 CG2 A:ILE82 3.7 20.5 1.0 C34 A:7OA400 3.7 15.6 0.5 O B:HOH162 3.9 41.2 1.0 O B:HOH140 3.9 17.9 1.0 C59 A:7OA400 4.0 13.0 0.5 CZ A:ARG8 4.0 23.8 1.0 C08 A:7OA400 4.2 12.8 0.5 NH1 A:ARG8 4.3 23.9 1.0 O2 A:7OA400 4.3 13.9 0.5 C13 A:7OA400 4.4 13.2 0.5 C12 A:7OA400 4.4 12.5 0.5 CB A:ILE82 4.6 18.8 1.0 O A:HOH530 4.6 34.9 1.0 O23 A:7OA400 4.7 13.0 0.5 O A:HOH582 4.7 42.7 1.0 NE A:ARG8 4.7 19.9 1.0 O B:GLY27 4.8 11.1 1.0 F2 A:7OA400 4.8 18.4 0.5 C49 A:7OA400 4.8 13.4 0.5 C21 A:7OA400 4.9 13.0 0.5 CD2 A:LEU23 5.0 15.0 1.0

Fluorine binding site 2 out of 4 in the X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:16.6 occ:0.50 F1 A:7OA400 0.0 16.6 0.5 C33 A:7OA400 1.3 13.7 0.5 C06 A:7OA400 2.4 12.1 0.5 C35 A:7OA400 2.4 13.1 0.5 C11 A:7OA400 3.1 15.8 0.5 C15 A:7OA400 3.2 11.0 0.5 NH2 B:ARG8 3.6 22.5 1.0 CG2 B:ILE82 3.7 18.4 1.0 C07 A:7OA400 3.7 12.6 0.5 C34 A:7OA400 3.7 14.5 0.5 C59 A:7OA400 3.9 12.9 0.5 O A:HOH534 4.0 16.3 1.0 CZ B:ARG8 4.0 24.8 1.0 C08 A:7OA400 4.2 12.8 0.5 NH1 B:ARG8 4.3 23.9 1.0 O2 A:7OA400 4.3 15.1 0.5 C13 A:7OA400 4.4 12.7 0.5 C12 A:7OA400 4.5 12.4 0.5 CB B:ILE82 4.6 17.2 1.0 O23 A:7OA400 4.6 12.8 0.5 C49 A:7OA400 4.8 13.3 0.5 NE B:ARG8 4.8 18.9 1.0 F2 A:7OA400 4.8 19.9 0.5 C21 A:7OA400 4.9 13.5 0.5 O A:GLY27 4.9 11.7 1.0 CD1 B:ILE82 5.0 22.5 1.0

Fluorine binding site 3 out of 4 in the X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:18.4 occ:0.50 F2 A:7OA400 0.0 18.4 0.5 C34 A:7OA400 1.3 15.6 0.5 C08 A:7OA400 2.4 12.8 0.5 C35 A:7OA400 2.4 14.9 0.5 CD A:PRO81 2.9 23.6 1.0 CG A:PRO81 2.9 30.8 1.0 C B:GLY49 2.9 19.1 1.0 N B:ILE50 3.1 18.2 1.0 C14 A:7OA400 3.2 12.7 0.5 CA B:GLY49 3.2 17.8 1.0 O B:GLY49 3.4 20.4 1.0 CB A:PRO81 3.6 24.0 1.0 C07 A:7OA400 3.7 11.9 0.5 CD1 B:ILE50 3.7 29.1 1.0 C33 A:7OA400 3.7 15.5 0.5 CA B:ILE50 3.8 18.4 1.0 CG1 B:ILE50 4.0 23.4 1.0 N A:PRO81 4.1 25.0 1.0 C15 A:7OA400 4.1 11.6 0.5 C06 A:7OA400 4.2 13.4 0.5 C13 A:7OA400 4.2 13.2 0.5 N B:GLY49 4.2 16.6 1.0 OG1 A:THR80 4.4 17.6 1.0 CA A:PRO81 4.5 26.2 1.0 O22 A:7OA400 4.5 11.2 0.5 CB B:ILE50 4.6 20.3 1.0 O B:GLY48 4.6 19.3 1.0 O B:HOH171 4.7 29.8 1.0 O A:HOH507 4.7 15.6 1.0 C B:GLY48 4.7 15.4 1.0 F1 A:7OA400 4.8 18.4 0.5 C12 A:7OA400 4.8 12.5 0.5 O9 A:7OA400 4.9 11.9 0.5 O10 A:7OA400 4.9 12.9 0.5 C32 A:7OA400 4.9 12.8 0.5 N A:ILE82 5.0 18.1 1.0

Fluorine binding site 4 out of 4 in the X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Crystal Structure of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:19.9 occ:0.50 F2 A:7OA400 0.0 19.9 0.5 C34 A:7OA400 1.3 14.5 0.5 C08 A:7OA400 2.4 12.8 0.5 C35 A:7OA400 2.4 13.1 0.5 CD B:PRO81 2.9 24.1 1.0 C A:GLY49 2.9 17.8 1.0 CG B:PRO81 2.9 23.7 1.0 N A:ILE50 3.0 19.0 1.0 CA A:GLY49 3.2 17.5 1.0 C14 A:7OA400 3.3 13.0 0.5 O A:GLY49 3.4 18.6 1.0 CD1 A:ILE50 3.4 30.3 1.0 C07 A:7OA400 3.7 12.6 0.5 C33 A:7OA400 3.7 13.7 0.5 CA A:ILE50 3.7 18.3 1.0 CG1 A:ILE50 3.9 24.3 1.0 C15 A:7OA400 4.1 11.0 0.5 C06 A:7OA400 4.2 12.1 0.5 N A:GLY49 4.2 17.8 1.0 N B:PRO81 4.3 26.8 1.0 C13 A:7OA400 4.3 12.7 0.5 OG1 B:THR80 4.3 17.5 1.0 CB B:PRO81 4.4 29.9 1.0 CB A:ILE50 4.4 22.5 1.0 O A:HOH552 4.5 27.6 1.0 O22 A:7OA400 4.5 11.9 0.5 O A:GLY48 4.7 17.3 1.0 O A:HOH507 4.7 15.6 1.0 C A:GLY48 4.8 16.0 1.0 O9 A:7OA400 4.8 12.4 0.5 F1 A:7OA400 4.8 16.6 0.5 C12 A:7OA400 4.8 12.4 0.5 C32 A:7OA400 5.0 12.7 0.5 CA B:PRO81 5.0 26.6 1.0 O10 A:7OA400 5.0 12.9 0.5

R.S.Yedidi, H.Hayashi, D.Das, H.Mitsuya. Structure-Function Analysis of Darunavir-Resistant-P51 Hiv-1 Protease in Complex with Grl-142. To Be Published.