Fluorine in PDB 6d0d: X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-087-13

The structure of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-087-13, PDB code: 6d0d 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)	31.30 / 1.85
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	62.592, 62.592, 82.372, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 23.4

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-087-13 (pdb code 6d0d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-087-13, PDB code: 6d0d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-087-13


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-087-13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F400 b:22.6 occ:0.48 F01 B:FQ4400 0.0 22.6 0.5 C35 B:FQ4400 1.3 20.1 0.5 C33 B:FQ4400 2.3 17.6 0.5 C34 B:FQ4400 2.4 17.9 0.5 CG A:PRO81 3.0 29.2 1.0 CB A:PRO81 3.4 23.3 1.0 O B:HOH557 3.5 39.5 1.0 C06 B:FQ4400 3.6 18.1 0.5 C08 B:FQ4400 3.6 16.7 0.5 O B:HOH589 3.7 32.9 1.0 CG1 A:VAL82 4.0 31.4 1.0 C30 B:FQ4400 4.1 17.5 0.5 C15 B:FQ4400 4.2 17.7 0.5 C07 B:FQ4400 4.2 16.3 0.5 CG2 A:VAL82 4.2 23.8 1.0 O B:GLY48 4.3 23.7 0.9 C14 B:FQ4400 4.4 18.1 0.5 CD A:PRO81 4.4 23.3 1.0 CA B:GLY49 4.6 20.2 1.0 CA A:PRO81 4.6 28.2 1.0 C A:PRO81 4.7 31.4 1.0 C B:GLY49 4.7 24.0 1.0 C13 B:FQ4400 4.7 16.3 0.5 CB A:VAL82 4.7 27.6 1.0 N A:VAL82 4.7 24.8 1.0 O B:GLY49 4.8 21.2 1.0 C29 B:FQ4400 4.8 18.6 0.5 C B:GLY48 4.8 24.3 0.9 C12 B:FQ4400 4.9 16.7 0.5 N A:PRO81 5.0 26.3 1.0 O B:HOH561 5.0 31.7 1.0

Fluorine binding site 2 out of 2 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-087-13


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-087-13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F400 b:23.8 occ:0.52 F01 B:FQ4400 0.0 23.8 0.5 C35 B:FQ4400 1.3 20.0 0.5 C33 B:FQ4400 2.3 20.5 0.5 C34 B:FQ4400 2.4 18.7 0.5 C14 B:FQ4400 2.8 20.8 0.5 CG B:PRO81 3.0 27.9 1.0 CB B:PRO81 3.4 22.6 1.0 C06 B:FQ4400 3.6 18.5 0.5 C08 B:FQ4400 3.6 16.6 0.5 CG1 B:VAL82 3.8 28.9 1.0 CG2 B:VAL82 4.1 24.7 1.0 C30 B:FQ4400 4.2 16.7 0.5 C07 B:FQ4400 4.2 16.4 0.5 C13 B:FQ4400 4.3 16.6 0.5 CD B:PRO81 4.4 23.5 1.0 O A:GLY48 4.4 19.8 1.0 CA B:PRO81 4.5 26.2 1.0 CB B:VAL82 4.6 26.3 1.0 C B:PRO81 4.6 29.3 1.0 N B:VAL82 4.6 24.4 1.0 CA A:GLY49 4.7 21.1 1.0 C29 B:FQ4400 4.7 18.2 0.5 C A:GLY49 4.8 21.4 1.0 O B:HOH541 4.8 24.7 1.0 C12 B:FQ4400 4.9 17.1 0.5 O A:GLY49 4.9 21.9 1.0 C A:GLY48 4.9 20.7 1.0 N B:PRO81 5.0 25.8 1.0

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