Fluorine in PDB 1dif: Hiv-1 Protease in Complex with A Difluoroketone Containing Inhibitor A79285

The structure of Hiv-1 Protease in Complex with A Difluoroketone Containing Inhibitor A79285, PDB code: 1dif was solved by A.M.Silva, R.E.Cachau, H.L.Sham, J.W.Erickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.000, 59.900, 62.100, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / n/a

The binding sites of Fluorine atom in the Hiv-1 Protease in Complex with A Difluoroketone Containing Inhibitor A79285 (pdb code 1dif). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-1 Protease in Complex with A Difluoroketone Containing Inhibitor A79285, PDB code: 1dif:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-1 Protease in Complex with A Difluoroketone Containing Inhibitor A79285


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 A Difluoroketone Containing Inhibitor A79285 within 5.0Å range: probe atom residue distance (Å) B Occ B:F101 b:21.4 occ:1.00 F1 B:A85101 0.0 21.4 1.0 C46 B:A85101 1.4 19.5 1.0 F2 B:A85101 2.1 19.7 1.0 H69 B:A85101 2.1 0.0 0.0 C49 B:A85101 2.3 19.4 1.0 C38 B:A85101 2.4 19.2 1.0 HA3 A:GLY27 2.4 0.0 0.0 H62 B:A85101 2.5 0.0 0.0 O48 B:A85101 2.5 17.6 1.0 C39 B:A85101 2.8 19.4 1.0 O47 B:A85101 2.9 19.8 1.0 N37 B:A85101 3.0 17.9 1.0 H59 B:A85101 3.0 0.0 0.0 OD1 A:ASP25 3.0 11.8 1.0 C A:GLY27 3.0 13.6 1.0 H61 B:A85101 3.1 0.0 0.0 OD2 B:ASP25 3.1 14.9 1.0 CA A:GLY27 3.1 12.7 1.0 H60 B:A85101 3.3 0.0 0.0 OD1 B:ASP25 3.3 14.3 1.0 O A:GLY27 3.3 14.6 1.0 OD2 A:ASP25 3.4 14.3 1.0 H68 B:A85101 3.4 0.0 0.0 N A:ALA28 3.4 12.4 1.0 CG B:ASP25 3.5 14.5 1.0 CG A:ASP25 3.6 13.6 1.0 HB3 A:ALA28 3.6 0.0 0.0 H A:GLY27 3.6 0.0 0.0 C51 B:A85101 3.7 18.0 1.0 N A:GLY27 3.8 13.2 1.0 H A:ALA28 3.8 0.0 0.0 HA A:ALA28 3.9 0.0 0.0 H73 B:A85101 3.9 0.0 0.0 HA2 A:GLY27 4.0 0.0 0.0 CA A:ALA28 4.0 13.3 1.0 C23 B:A85101 4.1 17.4 1.0 H74 B:A85101 4.1 0.0 0.0 C40 B:A85101 4.2 20.2 1.0 C52 B:A85101 4.3 18.6 1.0 CB A:ALA28 4.4 12.8 1.0 HD23 B:LEU23 4.4 0.0 0.0 H75 B:A85101 4.4 0.0 0.0 H63 B:A85101 4.4 0.0 0.0 HA3 B:GLY27 4.5 0.0 0.0 H29 B:A85101 4.5 0.0 0.0 HD22 B:LEU23 4.6 0.0 0.0 H B:GLY27 4.7 0.0 0.0 O24 B:A85101 4.7 15.3 1.0 N50 B:A85101 4.7 18.4 1.0 C41 B:A85101 4.8 22.6 1.0 CB B:ASP25 4.9 12.8 1.0 HB1 A:ALA28 4.9 0.0 0.0 C22 B:A85101 4.9 16.6 1.0 HB2 B:ASP25 5.0 0.0 0.0

Fluorine binding site 2 out of 2 in the Hiv-1 Protease in Complex with A Difluoroketone Containing Inhibitor A79285


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 A Difluoroketone Containing Inhibitor A79285 within 5.0Å range: probe atom residue distance (Å) B Occ B:F101 b:19.7 occ:1.00 F2 B:A85101 0.0 19.7 1.0 C46 B:A85101 1.3 19.5 1.0 F1 B:A85101 2.1 21.4 1.0 C49 B:A85101 2.3 19.4 1.0 H74 B:A85101 2.4 0.0 0.0 C38 B:A85101 2.4 19.2 1.0 H69 B:A85101 2.4 0.0 0.0 N37 B:A85101 2.6 17.9 1.0 OD2 A:ASP25 2.6 14.3 1.0 H73 B:A85101 2.7 0.0 0.0 C51 B:A85101 2.7 18.0 1.0 H60 B:A85101 2.8 0.0 0.0 O48 B:A85101 2.9 17.6 1.0 HB3 A:ALA28 2.9 0.0 0.0 C52 B:A85101 2.9 18.6 1.0 C23 B:A85101 3.0 17.4 1.0 H59 B:A85101 3.1 0.0 0.0 H32 B:A85101 3.2 0.0 0.0 O24 B:A85101 3.4 15.3 1.0 H75 B:A85101 3.4 0.0 0.0 HD12 A:ILE84 3.5 0.0 0.0 O47 B:A85101 3.5 19.8 1.0 CG A:ASP25 3.5 13.6 1.0 H31 B:A85101 3.5 0.0 0.0 H29 B:A85101 3.6 0.0 0.0 C39 B:A85101 3.7 19.4 1.0 H68 B:A85101 3.7 0.0 0.0 OD1 A:ASP25 3.7 11.8 1.0 C26 B:A85101 3.8 17.6 1.0 H62 B:A85101 3.9 0.0 0.0 CB A:ALA28 3.9 12.8 1.0 C22 B:A85101 3.9 16.6 1.0 HA A:ALA28 4.0 0.0 0.0 H76 B:A85101 4.0 0.0 0.0 HG23 A:ILE84 4.1 0.0 0.0 H2 B:HOH102 4.1 0.0 0.0 N50 B:A85101 4.2 18.4 1.0 H61 B:A85101 4.2 0.0 0.0 C53 B:A85101 4.2 18.8 1.0 N A:ALA28 4.2 12.4 1.0 CA A:ALA28 4.2 13.3 1.0 HB2 A:ALA28 4.4 0.0 0.0 C A:GLY27 4.4 13.6 1.0 HA3 A:GLY27 4.5 0.0 0.0 CD1 A:ILE84 4.5 17.3 1.0 C25 B:A85101 4.5 17.1 1.0 HB1 A:ALA28 4.6 0.0 0.0 C54 B:A85101 4.6 19.7 1.0 O A:GLY27 4.6 14.6 1.0 HG22 A:ILE84 4.6 0.0 0.0 HA3 B:GLY27 4.6 0.0 0.0 H1 B:HOH102 4.7 0.0 0.0 H A:ALA28 4.7 0.0 0.0 H72 B:A85101 4.7 0.0 0.0 HD13 A:ILE84 4.7 0.0 0.0 H33 B:A85101 4.7 0.0 0.0 C40 B:A85101 4.8 20.2 1.0 OD2 B:ASP25 4.9 14.9 1.0 O B:HOH102 4.9 16.1 1.0 CG2 A:ILE84 4.9 16.1 1.0 CB A:ASP25 4.9 12.7 1.0 OD1 B:ASP25 4.9 14.3 1.0 CA A:GLY27 5.0 12.7 1.0 O84 B:A85101 5.0 17.1 1.0 HB3 A:ASP25 5.0 0.0 0.0

A.M.Silva, R.E.Cachau, H.L.Sham, J.W.Erickson. Inhibition and Catalytic Mechanism of Hiv-1 Aspartic Protease. J.Mol.Biol. V. 255 321 1996.
ISSN: ISSN 0022-2836
PubMed: 8551523
DOI: 10.1006/JMBI.1996.0026