Chlorine in PDB 6vlm: Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit

The structure of Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit, PDB code: 6vlm was solved by D.J.Klein, J.M.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.86 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.900, 66.770, 57.430, 90.00, 102.33, 90.00
R / Rfree (%)	18 / 21.4

The binding sites of Chlorine atom in the Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit (pdb code 6vlm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit, PDB code: 6vlm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:50.0 occ:1.00 CL A:R2D301 0.0 50.0 1.0 C18 A:R2D301 1.7 53.2 1.0 C14 A:R2D301 2.7 52.8 1.0 C15 A:R2D301 2.7 55.3 1.0 CG B:TRP132 3.4 37.8 1.0 CB B:TRP132 3.6 36.7 1.0 CD2 B:TRP132 3.8 37.3 1.0 CD1 B:TRP132 3.8 40.9 1.0 C12 B:R2D302 3.8 71.7 1.0 C16 B:R2D302 3.9 71.7 1.0 CD2 B:LEU102 3.9 51.4 1.0 C9 A:R2D301 3.9 53.4 1.0 C10 A:R2D301 4.0 55.7 1.0 SD A:MET178 4.2 47.6 1.0 CD1 B:LEU102 4.2 48.0 1.0 CG A:MET178 4.3 43.1 1.0 CA B:ALA129 4.3 34.2 1.0 CE3 B:TRP132 4.3 38.0 1.0 CE A:MET178 4.3 44.6 1.0 CE2 B:TRP132 4.3 42.0 1.0 NE1 B:TRP132 4.4 40.6 1.0 C4 A:R2D301 4.4 56.4 1.0 O B:ALA128 4.5 40.3 1.0 CG B:LEU102 4.6 48.5 1.0 N B:ALA129 4.7 34.2 1.0 C B:ALA128 4.8 40.1 1.0 CB B:ALA129 4.9 34.7 1.0

Chlorine binding site 2 out of 3 in the Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:56.6 occ:1.00 CL B:R2D301 0.0 56.6 1.0 C18 B:R2D301 1.7 53.4 1.0 C14 B:R2D301 2.7 51.7 1.0 C15 B:R2D301 2.7 52.8 1.0 CB A:TRP132 3.5 41.3 1.0 CG A:TRP132 3.6 42.4 1.0 C9 B:R2D301 4.0 51.4 1.0 CD2 A:TRP132 4.0 42.3 1.0 C10 B:R2D301 4.0 51.9 1.0 CD1 A:TRP132 4.1 45.1 1.0 CD2 A:LEU102 4.1 50.2 1.0 CD1 A:LEU102 4.2 49.0 1.0 CA A:ALA129 4.2 41.0 1.0 SD B:MET178 4.3 47.5 1.0 CE B:MET178 4.3 43.7 1.0 O A:ALA128 4.4 46.7 1.0 CE3 A:TRP132 4.4 43.2 1.0 CG B:MET178 4.5 42.6 1.0 C4 B:R2D301 4.5 52.8 1.0 CE2 A:TRP132 4.7 46.1 1.0 NE1 A:TRP132 4.7 44.8 1.0 CG A:LEU102 4.7 48.4 1.0 N A:ALA129 4.7 41.1 1.0 C A:ALA128 4.8 45.4 1.0 CB A:ALA129 4.9 42.3 1.0 O A:ALA129 4.9 40.9 1.0 CG2 B:THR174 5.0 43.9 1.0

Chlorine binding site 3 out of 3 in the Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Core Catalytic Domain of Hiv Integrase in Complex with Virtual Screening Hit within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:67.1 occ:1.00 CL B:R2D302 0.0 67.1 1.0 C18 B:R2D302 1.7 64.0 1.0 C15 B:R2D302 2.7 62.9 1.0 C14 B:R2D302 2.7 61.8 1.0 N B:ALA128 3.5 40.1 1.0 CB B:LYS127 3.6 45.9 1.0 C B:LYS127 3.8 47.1 1.0 CA B:ALA128 3.8 39.5 1.0 O B:THR124 3.9 50.9 1.0 C10 B:R2D302 4.0 63.5 1.0 C9 B:R2D302 4.0 62.5 1.0 CB B:ALA128 4.2 40.4 1.0 O B:LYS127 4.2 47.6 1.0 CA B:LYS127 4.3 43.8 1.0 CG2 B:THR124 4.4 61.1 1.0 C4 B:R2D302 4.5 67.0 1.0 CG B:LYS127 4.9 53.7 1.0 C B:THR124 4.9 52.4 1.0 CD B:LYS127 4.9 63.4 1.0

X.C.Yan, J.M.Sanders, Y.D.Gao, M.Tudor, A.M.Haidle, D.J.Klein, A.Converso, C.A.Lesburg, Y.Zang, H.B.Wood. Augmenting Hit Identification By Virtual Screening Techniques in Small Molecule Drug Discovery. J.Chem.Inf.Model. 2020.
ISSN: ESSN 1549-960X
PubMed: 32309939
DOI: 10.1021/ACS.JCIM.0C00113