Fluorine in PDB 6uwb: X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-08513

The structure of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-08513, PDB code: 6uwb was solved by R.S.Yedidi, H.Hayashi, A.K.Ghosh, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.40 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	62.918, 62.918, 82.112, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 26.3

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-08513 (pdb code 6uwb). 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-08513, PDB code: 6uwb:
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-08513


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-08513 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:31.7 occ:0.49 F46 A:QJY400 0.0 31.7 0.5 C39 A:QJY400 1.3 30.3 0.5 C12 A:QJY400 2.3 28.4 0.5 C41 A:QJY400 2.4 28.2 0.5 CG B:PRO81 2.9 38.5 1.0 CD B:PRO81 3.0 37.0 1.0 N A:ILE50 3.0 29.7 1.0 C A:GLY49 3.0 32.1 1.0 C22 A:QJY400 3.1 28.3 0.5 CA A:ILE50 3.4 33.0 1.0 CA A:GLY49 3.5 31.7 1.0 O A:GLY49 3.5 28.6 1.0 C14 A:QJY400 3.6 29.4 0.5 C40 A:QJY400 3.6 28.9 0.5 CG1 A:ILE50 3.8 35.2 1.0 C23 A:QJY400 4.1 29.0 0.5 CD1 A:ILE50 4.1 38.5 1.0 C15 A:QJY400 4.1 29.0 0.5 C21 A:QJY400 4.2 29.1 0.5 CB A:ILE50 4.2 32.4 1.0 CB B:PRO81 4.3 37.8 1.0 N B:PRO81 4.3 36.0 1.0 OG1 B:THR80 4.4 34.1 1.0 N A:GLY49 4.6 29.9 1.0 C A:ILE50 4.6 37.7 1.0 O A:HOH504 4.7 28.1 1.0 O18 A:QJY400 4.7 27.7 0.5 C20 A:QJY400 4.7 27.9 0.5 F47 A:QJY400 4.8 31.2 0.5 C38 A:QJY400 4.9 27.4 0.5 O A:ILE50 4.9 42.4 1.0 O17 A:QJY400 4.9 28.3 0.5 CA B:PRO81 5.0 42.3 1.0 O30 A:QJY400 5.0 25.9 0.5 N B:VAL82 5.0 42.2 1.0 CG2 B:VAL82 5.0 33.7 1.0

Fluorine binding site 2 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-08513


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-08513 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:33.1 occ:0.51 F46 A:QJY400 0.0 33.1 0.5 C39 A:QJY400 1.3 31.0 0.5 C12 A:QJY400 2.3 29.3 0.5 C41 A:QJY400 2.3 28.7 0.5 CG A:PRO81 2.9 36.6 1.0 C B:GLY49 2.9 34.4 1.0 C22 A:QJY400 3.0 28.5 0.5 N B:ILE50 3.1 32.0 1.0 CD A:PRO81 3.2 35.7 1.0 O B:GLY49 3.2 33.1 1.0 CA B:GLY49 3.4 31.4 1.0 CA B:ILE50 3.5 35.3 1.0 C14 A:QJY400 3.6 29.2 0.5 C40 A:QJY400 3.6 30.0 0.5 C23 A:QJY400 4.0 29.9 0.5 C21 A:QJY400 4.0 29.1 0.5 C15 A:QJY400 4.1 30.0 0.5 CD1 B:ILE50 4.2 38.0 1.0 CB B:ILE50 4.2 30.7 1.0 CB A:PRO81 4.4 34.2 1.0 N B:GLY49 4.4 30.5 1.0 N A:PRO81 4.5 32.4 1.0 C20 A:QJY400 4.6 28.3 0.5 O18 A:QJY400 4.6 28.8 0.5 OG1 A:THR80 4.6 30.7 1.0 O A:HOH504 4.7 28.1 1.0 CG1 B:ILE50 4.7 41.5 1.0 C B:ILE50 4.7 39.1 1.0 O B:GLY48 4.7 31.6 1.0 F47 A:QJY400 4.7 34.9 0.5 C38 A:QJY400 4.8 28.1 0.5 O30 A:QJY400 4.8 27.8 0.5 C B:GLY48 4.9 31.4 1.0 O B:HOH116 4.9 35.4 1.0 O17 A:QJY400 5.0 28.0 0.5

Fluorine binding site 3 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-08513


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-08513 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:31.2 occ:0.49 F47 A:QJY400 0.0 31.2 0.5 C40 A:QJY400 1.4 28.9 0.5 C15 A:QJY400 2.4 29.0 0.5 C41 A:QJY400 2.4 28.2 0.5 C23 A:QJY400 2.5 29.0 0.5 C35 A:QJY400 3.1 26.8 0.5 C36 A:QJY400 3.3 27.7 0.5 NH2 B:ARG8 3.5 34.2 1.0 CG2 B:VAL82 3.6 33.7 1.0 CG1 B:VAL82 3.6 40.3 1.0 C14 A:QJY400 3.7 29.4 0.5 C39 A:QJY400 3.7 30.3 0.5 CZ B:ARG8 3.8 41.4 1.0 O A:HOH514 3.8 32.7 1.0 NH1 B:ARG8 3.9 39.8 1.0 C21 A:QJY400 3.9 29.1 0.5 C20 A:QJY400 4.2 27.9 0.5 C12 A:QJY400 4.2 28.4 0.5 CB B:VAL82 4.3 39.0 1.0 O34 A:QJY400 4.5 26.8 0.5 CD1 B:LEU23 4.5 32.6 1.0 NE B:ARG8 4.6 39.9 1.0 O A:GLY27 4.6 26.1 1.0 C22 A:QJY400 4.7 28.3 0.5 F46 A:QJY400 4.8 31.7 0.5 C37 A:QJY400 4.8 27.5 0.5 C38 A:QJY400 4.9 27.4 0.5

Fluorine binding site 4 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-08513


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-08513 within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:34.9 occ:0.51 F47 A:QJY400 0.0 34.9 0.5 C40 A:QJY400 1.4 30.0 0.5 C15 A:QJY400 2.4 30.0 0.5 C41 A:QJY400 2.4 28.7 0.5 C23 A:QJY400 2.5 29.9 0.5 CG2 A:VAL82 3.1 42.3 1.0 C35 A:QJY400 3.2 28.6 0.5 NH2 A:ARG8 3.5 31.9 1.0 NH1 A:ARG8 3.5 44.8 1.0 C36 A:QJY400 3.5 28.9 0.5 O B:HOH114 3.6 34.9 1.0 CZ A:ARG8 3.6 42.5 1.0 C14 A:QJY400 3.6 29.2 0.5 C39 A:QJY400 3.7 31.0 0.5 CB A:VAL82 3.8 38.0 1.0 C21 A:QJY400 3.9 29.1 0.5 C12 A:QJY400 4.1 29.3 0.5 CG1 A:VAL82 4.2 34.5 1.0 C20 A:QJY400 4.2 28.3 0.5 CD2 A:LEU23 4.5 28.4 1.0 NE A:ARG8 4.5 41.0 1.0 O34 A:QJY400 4.6 27.6 0.5 O B:GLY27 4.7 28.1 1.0 C22 A:QJY400 4.7 28.5 0.5 F46 A:QJY400 4.7 33.1 0.5 C38 A:QJY400 4.9 28.1 0.5

M.Amano, R.S.Yedidi, P.M.Salcedo-Gomez, H.Hayashi, K.Hasegawa, C.D.Martyr, A.K.Ghosh, H.Mitsuya. Fluoride-Modifications Contribute to Potent Anti-Hiv Activity Against Drug-Resistant Hiv-1 and Favorable Blood-Brain Barrier Penetration Property of Novel Central Nervous System (Cns)-Targeting Hiv-1 Protease Inhibitors (Pis) in Vitro. To Be Published.