Fluorine in PDB 8cbv: Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916, PDB code: 8cbv was solved by M.R.Singer, V.E.Pye, Z.Yu, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.11 / 1.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.275, 65.083, 70.588, 90, 101.64, 90
R / Rfree (%)	18.7 / 23

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 (pdb code 8cbv). 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 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916, PDB code: 8cbv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 within 5.0Å range: probe atom residue distance (Å) B Occ B:F506 b:40.7 occ:1.00 F30 B:U5S506 0.0 40.7 1.0 C10 B:U5S506 1.3 38.7 1.0 C09 B:U5S506 2.3 33.5 1.0 C04 B:U5S506 2.4 35.2 1.0 O05 B:U5S506 2.7 33.5 1.0 CB D:ALA129 3.0 29.9 1.0 CA D:ALA129 3.2 33.3 1.0 N D:ALA129 3.3 35.7 1.0 CB D:ALA98 3.6 28.3 1.0 C08 B:U5S506 3.6 37.3 1.0 O D:THR125 3.6 36.0 0.3 C03 B:U5S506 3.6 37.8 1.0 O D:THR125 3.7 35.2 0.7 CD1 D:LEU102 3.9 33.6 1.0 C27 B:U5S506 3.9 38.5 1.0 CG D:LEU102 4.0 32.1 1.0 C06 B:U5S506 4.1 31.3 1.0 C07 B:U5S506 4.1 34.8 1.0 C D:ALA128 4.2 36.7 1.0 CD2 D:LEU102 4.3 31.7 1.0 O D:ALA98 4.5 27.7 1.0 C D:ALA98 4.6 28.6 1.0 CA D:ALA98 4.6 27.7 1.0 CB D:ALA128 4.6 34.5 1.0 C26 B:U5S506 4.7 40.3 1.0 C D:ALA129 4.7 34.9 1.0 O D:ALA128 4.7 34.0 1.0 C D:THR125 4.8 34.1 0.3 C02 B:U5S506 4.8 33.4 1.0 CG2 D:THR125 4.8 31.5 0.7 C11 B:U5S506 4.8 34.9 1.0 C D:THR125 4.8 33.9 0.7 C01 B:U5S506 5.0 32.1 1.0

Fluorine binding site 2 out of 2 in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:39.1 occ:1.00 F30 D:U5S501 0.0 39.1 1.0 C10 D:U5S501 1.4 36.4 1.0 C09 D:U5S501 2.4 33.3 1.0 C04 D:U5S501 2.4 33.2 1.0 O05 D:U5S501 2.7 33.0 1.0 CB B:ALA129 3.0 30.3 1.0 CA B:ALA129 3.3 33.1 1.0 CD1 B:LEU102 3.5 31.7 1.0 N B:ALA129 3.6 32.3 1.0 CB B:ALA98 3.6 30.2 1.0 C08 D:U5S501 3.7 35.9 1.0 C03 D:U5S501 3.7 31.7 1.0 CG B:LEU102 3.8 33.7 1.0 C27 D:U5S501 3.9 31.9 1.0 O B:THR125 3.9 30.0 0.2 O B:THR125 4.0 29.9 0.8 C06 D:U5S501 4.0 29.2 1.0 CD2 B:LEU102 4.1 34.4 1.0 C07 D:U5S501 4.2 31.5 1.0 O B:ALA98 4.3 27.0 1.0 C B:ALA128 4.5 34.9 1.0 C B:ALA98 4.5 27.4 1.0 CA B:ALA98 4.6 29.9 1.0 C B:ALA129 4.8 34.5 1.0 C26 D:U5S501 4.8 39.1 1.0 C02 D:U5S501 4.8 33.8 1.0 C11 D:U5S501 4.9 34.8 1.0 CG2 B:THR125 4.9 31.4 0.8 C01 D:U5S501 4.9 30.1 1.0 CB B:ALA128 5.0 32.4 1.0 O B:ALA128 5.0 33.0 1.0

D.Bonnard, E.Le Rouzic, M.R.Singer, Z.Yu, F.Le Strat, C.Batisse, J.Batisse, C.Amadori, S.Chasset, V.E.Pye, S.Emiliani, B.Ledoussal, M.Ruff, F.Moreau, P.Cherepanov, R.Benarousa. Biological and Structural Analyses of New Potent Allosteric Inhibitors of Hiv-1 Integrase Antimicrob.Agents Chemother. 2023.
ISSN: ESSN 1098-6596