Chlorine in PDB 8bdt: Ternary Complex Between Vcb, BRD4-BD2 and Protac 51

The structure of Ternary Complex Between Vcb, BRD4-BD2 and Protac 51, PDB code: 8bdt was solved by F.J.Sorrell, J.E.Mueller, M.Lehmann, A.A.Wegener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.80 / 2.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.483, 82.483, 169.088, 90, 90, 120
R / Rfree (%)	18.8 / 24.3

The binding sites of Chlorine atom in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 51 (pdb code 8bdt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 51, PDB code: 8bdt:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 51


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Between Vcb, BRD4-BD2 and Protac 51 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:77.2 occ:1.00 CL D:QLX301 0.0 77.2 1.0 C37 D:QLX301 1.7 72.0 1.0 C38 D:QLX301 2.7 72.3 1.0 C36 D:QLX301 2.7 70.4 1.0 C53 D:QLX301 3.2 72.5 1.0 CD A:GLU438 3.6 87.2 1.0 NH2 D:ARG69 3.6 73.4 0.3 OE1 A:GLU438 3.7 87.0 1.0 NH2 D:ARG69 3.8 77.7 0.7 OE2 A:GLU438 3.9 89.9 1.0 C39 D:QLX301 4.0 73.0 1.0 C35 D:QLX301 4.0 69.7 1.0 CG A:GLU438 4.0 82.9 1.0 SD A:MET442 4.1 71.7 1.0 CB A:GLU438 4.2 78.4 1.0 C52 D:QLX301 4.4 72.8 1.0 C34 D:QLX301 4.5 69.6 1.0 CZ D:ARG69 4.6 74.0 0.3 CZ D:ARG69 4.8 80.7 0.7 CZ2 A:TRP374 4.8 73.6 1.0 C51 D:QLX301 4.9 70.4 1.0 OH D:TYR112 4.9 79.9 1.0 NE D:ARG69 4.9 76.8 0.3 CE A:MET442 4.9 71.8 1.0

Chlorine binding site 2 out of 2 in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 51


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Between Vcb, BRD4-BD2 and Protac 51 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:73.8 occ:1.00 CL H:QLX301 0.0 73.8 1.0 C37 H:QLX301 1.7 61.8 1.0 C38 H:QLX301 2.7 60.1 1.0 C36 H:QLX301 2.7 61.8 1.0 CD E:GLU438 3.6 87.1 1.0 OE1 E:GLU438 3.6 90.4 1.0 OE2 E:GLU438 3.6 87.9 1.0 NH2 H:ARG69 3.8 91.0 1.0 SD E:MET442 3.9 64.0 1.0 CB E:GLU438 4.0 75.3 1.0 C39 H:QLX301 4.0 60.5 1.0 C35 H:QLX301 4.0 60.9 1.0 C53 H:QLX301 4.0 75.2 1.0 NH1 H:ARG69 4.2 98.0 1.0 CG E:GLU438 4.3 81.5 1.0 CZ H:ARG69 4.5 95.0 1.0 C34 H:QLX301 4.5 58.8 1.0 CE E:MET442 4.8 71.6 1.0 CZ2 E:TRP374 4.8 66.0 1.0 OH H:TYR112 5.0 67.8 1.0

J.Krieger, F.J.Sorell, A.A.Wegener, B.Leuthner, F.Machrouhi-Porcher, M.Hecht, E.M.Leibrock, J.E.Mueller, J.Eisert, I.V.Hartung, S.Schlesiger. Systematic Potency & Property Assessment of Vhl Ligands and Implications on Protac Design. Chemmedchem 2023.
ISSN: ESSN 1860-7187
PubMed: 36749883
DOI: 10.1002/CMDC.202200615