Fluorine in PDB 5tys: X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-142

The structure of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-142, PDB code: 5tys was solved by R.S.Yedidi, H.Hayashi, M.Aoki, D.Das, A.K.Ghosh, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.86 / 2.01
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	63.131, 63.131, 82.229, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.7

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-142 (pdb code 5tys). 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 Wild Type Hiv-1 Protease in Complex with Grl-142, PDB code: 5tys:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the X-Ray Crystal Structure of Wild Type 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 Wild Type Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:23.7 occ:0.47 F1 A:7OA400 0.0 23.7 0.5 C33 A:7OA400 1.4 22.4 0.5 C06 A:7OA400 2.4 21.2 0.5 C35 A:7OA400 2.4 20.7 0.5 C14 A:7OA400 3.0 21.6 0.5 CG1 B:VAL82 3.3 31.2 1.0 C11 A:7OA400 3.3 19.2 0.5 NH2 B:ARG8 3.5 33.3 1.0 C07 A:7OA400 3.7 20.4 0.5 C34 A:7OA400 3.7 23.4 0.5 O B:HOH115 3.8 26.7 1.0 CZ B:ARG8 4.0 40.0 1.0 C59 A:7OA400 4.0 20.2 0.5 C12 A:7OA400 4.1 20.3 0.5 C08 A:7OA400 4.2 20.7 0.5 C13 A:7OA400 4.2 19.6 0.5 NH1 B:ARG8 4.3 39.3 1.0 CB B:VAL82 4.5 32.8 1.0 CG2 B:VAL82 4.6 29.5 1.0 O A:GLY27 4.7 19.7 1.0 O2 A:7OA400 4.7 20.4 0.5 NE B:ARG8 4.8 32.9 1.0 C49 A:7OA400 4.8 18.4 0.5 F2 A:7OA400 4.8 23.7 0.5 O23 A:7OA400 4.9 17.8 0.5 C32 A:7OA400 5.0 18.6 0.5

Fluorine binding site 2 out of 4 in the X-Ray Crystal Structure of Wild Type 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 Wild Type Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:24.4 occ:0.53 F1 A:7OA400 0.0 24.4 0.5 C33 A:7OA400 1.4 22.7 0.5 C06 A:7OA400 2.4 19.1 0.5 C35 A:7OA400 2.4 21.5 0.5 C11 A:7OA400 3.2 18.1 0.5 NH2 A:ARG8 3.4 29.2 1.0 C07 A:7OA400 3.7 20.4 0.5 C34 A:7OA400 3.7 22.8 0.5 C59 A:7OA400 3.8 19.7 0.5 CZ A:ARG8 3.9 37.0 1.0 O B:HOH111 3.9 25.2 1.0 NH1 A:ARG8 3.9 40.3 1.0 CG1 A:VAL82 3.9 29.4 1.0 C13 A:7OA400 4.0 20.4 0.5 C12 A:7OA400 4.0 19.9 0.5 C08 A:7OA400 4.2 20.1 0.5 CB A:VAL82 4.5 27.8 1.0 O2 A:7OA400 4.6 19.6 0.5 C14 A:7OA400 4.6 21.1 0.5 C49 A:7OA400 4.7 18.4 0.5 O23 A:7OA400 4.8 18.0 0.5 O B:GLY27 4.8 19.0 1.0 F2 A:7OA400 4.8 23.1 0.5 NE A:ARG8 4.9 34.0 1.0 C6 A:7OA400 4.9 18.4 0.5 C32 A:7OA400 5.0 18.6 0.5 CG2 A:VAL82 5.0 26.4 1.0

Fluorine binding site 3 out of 4 in the X-Ray Crystal Structure of Wild Type 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 Wild Type Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:23.7 occ:0.47 F2 A:7OA400 0.0 23.7 0.5 C34 A:7OA400 1.4 23.4 0.5 C08 A:7OA400 2.4 20.7 0.5 C35 A:7OA400 2.4 20.7 0.5 CG B:PRO81 2.8 29.8 1.0 N A:ILE50 3.0 21.2 1.0 C A:GLY49 3.0 24.3 1.0 CD B:PRO81 3.1 28.9 1.0 C15 A:7OA400 3.1 20.4 0.5 CA A:ILE50 3.4 25.7 1.0 CA A:GLY49 3.5 24.0 1.0 O A:GLY49 3.5 21.1 1.0 C07 A:7OA400 3.6 20.4 0.5 C33 A:7OA400 3.7 22.4 0.5 CG1 A:ILE50 3.8 32.8 1.0 C14 A:7OA400 4.0 21.6 0.5 C13 A:7OA400 4.1 19.6 0.5 CD1 A:ILE50 4.1 30.5 1.0 C06 A:7OA400 4.2 21.2 0.5 CB A:ILE50 4.2 26.0 1.0 CB B:PRO81 4.2 28.2 1.0 N B:PRO81 4.3 29.9 1.0 OG1 B:THR80 4.3 23.2 1.0 O A:HOH503 4.5 20.5 1.0 N A:GLY49 4.5 25.0 1.0 C12 A:7OA400 4.5 20.3 0.5 C A:ILE50 4.6 27.9 1.0 O10 A:7OA400 4.6 17.9 0.5 O9 A:7OA400 4.7 20.9 0.5 O22 A:7OA400 4.8 18.0 0.5 F1 A:7OA400 4.8 23.7 0.5 CA B:PRO81 4.9 31.3 1.0 C32 A:7OA400 4.9 18.6 0.5 N B:VAL82 4.9 28.9 1.0 CG1 B:VAL82 4.9 31.2 1.0 O A:ILE50 4.9 33.7 1.0 CD1 B:ILE84 5.0 26.4 1.0

Fluorine binding site 4 out of 4 in the X-Ray Crystal Structure of Wild Type 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 Wild Type Hiv-1 Protease in Complex with Grl-142 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:23.1 occ:0.53 F2 A:7OA400 0.0 23.1 0.5 C34 A:7OA400 1.4 22.8 0.5 C08 A:7OA400 2.4 20.1 0.5 C35 A:7OA400 2.4 21.5 0.5 CG A:PRO81 2.9 30.0 1.0 N B:ILE50 3.0 22.1 1.0 CD A:PRO81 3.0 26.8 1.0 C B:GLY49 3.1 26.2 1.0 CA B:ILE50 3.2 24.3 1.0 C15 A:7OA400 3.4 20.3 0.5 O B:GLY49 3.5 22.6 1.0 C07 A:7OA400 3.6 20.4 0.5 CA B:GLY49 3.7 24.6 1.0 C33 A:7OA400 3.7 22.7 0.5 CB B:ILE50 3.8 26.7 1.0 C13 A:7OA400 3.9 20.4 0.5 CG1 B:ILE50 3.9 25.7 1.0 C06 A:7OA400 4.2 19.1 0.5 OG1 A:THR80 4.2 23.9 1.0 CG1 A:VAL82 4.3 29.4 1.0 N A:PRO81 4.3 31.3 1.0 CB A:PRO81 4.3 28.0 1.0 C B:ILE50 4.5 30.1 1.0 O9 A:7OA400 4.6 20.3 0.5 O A:HOH503 4.6 20.5 1.0 C12 A:7OA400 4.7 19.9 0.5 N B:GLY49 4.7 24.1 1.0 F1 A:7OA400 4.8 24.4 0.5 O10 A:7OA400 4.9 19.8 0.5 O B:ILE50 4.9 34.4 1.0 N A:VAL82 4.9 28.1 1.0 CD1 B:ILE50 4.9 24.5 1.0 C32 A:7OA400 4.9 18.6 0.5 CA A:PRO81 4.9 32.3 1.0 CD1 A:ILE84 5.0 25.3 1.0

M.Aoki, H.Hayashi, K.V.Rao, D.Das, N.Higashi-Kuwata, H.Bulut, H.Aoki-Ogata, Y.Takamatsu, R.S.Yedidi, D.A.Davis, S.I.Hattori, N.Nishida, K.Hasegawa, N.Takamune, P.R.Nyalapatla, H.L.Osswald, H.Jono, H.Saito, R.Yarchoan, S.Misumi, A.K.Ghosh, H.Mitsuya. A Novel Central Nervous System-Penetrating Protease Inhibitor Overcomes Human Immunodeficiency Virus 1 Resistance with Unprecedented Am to Pm Potency. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 29039736
DOI: 10.7554/ELIFE.28020