Fluorine in PDB 6d0e: X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13

The structure of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13, PDB code: 6d0e 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)	31.34 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	62.686, 62.686, 82.181, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24.7

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13 (pdb code 6d0e). 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-084-13, PDB code: 6d0e:
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-084-13


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-084-13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:24.1 occ:0.52 F01 B:FQ1500 0.0 24.1 0.5 C33 B:FQ1500 1.3 20.0 0.5 C09 B:FQ1500 2.3 19.6 0.5 C06 B:FQ1500 2.3 19.5 0.5 CG A:PRO81 2.9 28.4 1.0 CD A:PRO81 3.1 28.6 1.0 C B:GLY49 3.1 24.6 1.0 N B:ILE50 3.2 20.0 1.0 C13 B:FQ1500 3.3 20.1 0.5 CA B:ILE50 3.4 23.6 1.0 O B:GLY49 3.5 21.5 1.0 CA B:GLY49 3.6 21.5 1.0 C15 B:FQ1500 3.6 18.4 0.5 C34 B:FQ1500 3.6 20.9 0.5 C07 B:FQ1500 3.6 20.1 0.5 C14 B:FQ1500 3.9 21.1 0.5 CB B:ILE50 4.1 24.1 1.0 C08 B:FQ1500 4.1 19.3 0.5 CG1 B:ILE50 4.3 28.2 1.0 CB A:PRO81 4.3 28.0 1.0 N A:PRO81 4.4 28.1 1.0 OG1 A:THR80 4.5 21.9 1.0 C12 B:FQ1500 4.5 18.9 0.5 N B:GLY49 4.5 19.9 1.0 C B:ILE50 4.6 29.0 1.0 F02 B:FQ1500 4.7 19.1 0.5 CG2 A:VAL82 4.8 23.8 0.3 O B:HOH601 4.8 17.3 1.0 C32 B:FQ1500 4.8 15.3 0.5 N A:VAL82 4.8 27.3 1.0 O22 B:FQ1500 4.9 17.0 0.5 O B:HOH621 4.9 36.0 1.0 O B:GLY48 4.9 19.9 0.9 O10 B:FQ1500 4.9 18.3 0.5 CA A:PRO81 4.9 33.0 1.0 CG2 A:VAL82 5.0 29.0 0.7

Fluorine binding site 2 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13


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-084-13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:23.7 occ:0.48 F01 B:FQ1500 0.0 23.7 0.5 C33 B:FQ1500 1.3 22.6 0.5 C06 B:FQ1500 2.3 19.5 0.5 C09 B:FQ1500 2.4 18.6 0.5 CG B:PRO81 2.8 31.5 1.0 N A:ILE50 3.0 21.7 1.0 C A:GLY49 3.0 25.8 1.0 CD B:PRO81 3.1 25.9 1.0 C13 B:FQ1500 3.3 20.8 0.5 CA A:ILE50 3.4 22.7 1.0 C15 B:FQ1500 3.4 19.8 0.5 CA A:GLY49 3.4 24.0 1.0 O A:GLY49 3.6 20.7 1.0 C07 B:FQ1500 3.6 20.2 0.5 C34 B:FQ1500 3.6 20.0 0.5 CG1 A:ILE50 3.8 27.5 1.0 CB A:ILE50 4.1 24.5 1.0 C14 B:FQ1500 4.1 21.3 0.5 C08 B:FQ1500 4.1 20.2 0.5 CB B:PRO81 4.3 28.6 1.0 N B:PRO81 4.4 29.1 1.0 OG1 B:THR80 4.5 20.8 1.0 C12 B:FQ1500 4.5 19.1 0.5 O B:HOH601 4.5 17.3 1.0 N A:GLY49 4.5 20.1 1.0 C A:ILE50 4.6 28.8 1.0 F02 B:FQ1500 4.7 19.2 0.5 O10 B:FQ1500 4.8 19.3 0.5 C32 B:FQ1500 4.8 16.7 0.5 O9 B:FQ1500 4.9 19.5 0.5 O22 B:FQ1500 4.9 18.5 0.5 N B:VAL82 4.9 30.6 1.0 CA B:PRO81 4.9 31.6 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-084-13


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-084-13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:19.1 occ:0.52 F02 B:FQ1500 0.0 19.1 0.5 C34 B:FQ1500 1.3 20.9 0.5 C09 B:FQ1500 2.3 19.6 0.5 C08 B:FQ1500 2.4 19.3 0.5 CG2 A:VAL82 3.1 29.0 0.7 C29 B:FQ1500 3.1 16.1 0.5 C14 B:FQ1500 3.2 21.1 0.5 CG1 A:VAL82 3.3 28.9 0.3 C30 B:FQ1500 3.3 18.0 0.5 NH2 A:ARG8 3.4 27.6 1.0 C33 B:FQ1500 3.6 20.0 0.5 C07 B:FQ1500 3.6 20.1 0.5 CG2 A:VAL82 3.7 23.8 0.3 O B:HOH615 3.7 22.9 1.0 CZ A:ARG8 3.8 36.1 1.0 C13 B:FQ1500 3.8 20.1 0.5 CB A:VAL82 3.9 27.0 0.7 NH1 A:ARG8 3.9 32.3 1.0 CB A:VAL82 4.0 27.0 0.3 C12 B:FQ1500 4.1 18.9 0.5 C06 B:FQ1500 4.1 19.5 0.5 CG1 A:VAL82 4.4 21.4 0.7 O28 B:FQ1500 4.5 15.7 0.5 O B:GLY27 4.6 19.4 1.0 NE A:ARG8 4.6 32.3 1.0 CD2 A:LEU23 4.7 18.6 1.0 F01 B:FQ1500 4.7 24.1 0.5 C31 B:FQ1500 4.9 17.3 0.5 C32 B:FQ1500 4.9 15.3 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-084-13


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-084-13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:19.2 occ:0.48 F02 B:FQ1500 0.0 19.2 0.5 C34 B:FQ1500 1.3 20.0 0.5 C08 B:FQ1500 2.3 20.2 0.5 C09 B:FQ1500 2.3 18.6 0.5 C14 B:FQ1500 3.1 21.3 0.5 C29 B:FQ1500 3.2 15.7 0.5 CG1 B:VAL82 3.4 35.2 1.0 C30 B:FQ1500 3.4 18.1 0.5 NH2 B:ARG8 3.5 30.8 1.0 CG2 B:VAL82 3.6 28.3 1.0 C33 B:FQ1500 3.6 22.6 0.5 C07 B:FQ1500 3.6 20.2 0.5 C13 B:FQ1500 3.7 20.8 0.5 O B:HOH623 3.7 25.7 1.0 CZ B:ARG8 3.9 37.8 1.0 NH1 B:ARG8 4.1 33.7 1.0 C12 B:FQ1500 4.1 19.1 0.5 C06 B:FQ1500 4.1 19.5 0.5 CB B:VAL82 4.1 35.4 1.0 CD1 B:LEU23 4.5 23.9 1.0 O28 B:FQ1500 4.6 16.2 0.5 NE B:ARG8 4.6 30.4 1.0 O A:GLY27 4.7 18.2 1.0 F01 B:FQ1500 4.7 23.7 0.5 C32 B:FQ1500 4.9 16.7 0.5 C31 B:FQ1500 4.9 17.6 0.5

M.Amano, P.M.Salcedo-Gomez, R.S.Yedidi, R.Zhao, H.Hayashi, K.Hasegawa, T.Nakamura, C.D.Martyr, A.K.Ghosh, H.Mitsuya. Novel Central Nervous System (Cns)-Targeting Protease Inhibitors For Drug-Resistant Hiv Infection and Hiv-Associated Cns Complications. Antimicrob.Agents Chemother. V. 63 2019.
ISSN: ESSN 1098-6596
PubMed: 31061155
DOI: 10.1128/AAC.00466-19