Chlorine in PDB 8bdx: Ternary Complex Between Vcb, BRD4-BD2 and Protac 48

The structure of Ternary Complex Between Vcb, BRD4-BD2 and Protac 48, PDB code: 8bdx was solved by F.J.Sorrell, J.E.Mueller, M.Lehmann, A.Wegener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.31 / 2.93
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.341, 82.341, 168.96, 90, 90, 120
R / Rfree (%)	18.5 / 25.8

The binding sites of Chlorine atom in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 48 (pdb code 8bdx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 48, PDB code: 8bdx:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 48


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 48 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:116.1 occ:1.00 CL30 D:QIY301 0.0 116.1 1.0 C29 D:QIY301 1.7 104.3 1.0 C31 D:QIY301 2.7 103.6 1.0 C28 D:QIY301 2.7 105.0 1.0 CD A:GLU438 3.5 114.3 1.0 NH1 D:ARG69 3.6 79.6 0.5 C63 D:QIY301 3.6 117.5 1.0 OE2 A:GLU438 3.6 120.4 1.0 OE1 A:GLU438 3.7 113.2 1.0 CG A:GLU438 3.8 112.8 1.0 SD A:MET442 3.9 103.3 1.0 C32 D:QIY301 4.0 98.3 1.0 C27 D:QIY301 4.0 102.2 1.0 NH1 D:ARG69 4.1 88.6 0.5 CB A:GLU438 4.2 104.3 1.0 CZ D:ARG69 4.4 87.9 0.5 C26 D:QIY301 4.5 96.1 1.0 NH2 D:ARG69 4.6 98.6 0.5 CZ D:ARG69 4.7 99.1 0.5 CZ2 A:TRP374 4.7 86.5 1.0 C62 D:QIY301 4.7 112.6 1.0 NH2 D:ARG69 4.8 81.8 0.5 CE A:MET442 4.8 93.3 1.0 C64 D:QIY301 5.0 110.5 1.0 OH D:TYR112 5.0 102.3 1.0 CH2 A:TRP374 5.0 91.3 1.0 N A:VAL439 5.0 90.3 1.0

Chlorine binding site 2 out of 4 in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 48


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 48 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:222.8 occ:1.00 CL38 D:QIY301 0.0 222.8 1.0 C39 D:QIY301 1.7 174.5 1.0 C40 D:QIY301 2.7 179.8 1.0 C42 D:QIY301 2.7 137.6 1.0 CD D:ARG107 3.7 123.2 1.0 NE D:ARG107 3.7 148.1 1.0 CG D:PRO99 3.9 91.7 1.0 C41 D:QIY301 4.0 152.0 1.0 C43 D:QIY301 4.0 123.6 1.0 CD D:PRO99 4.2 88.9 1.0 CA A:GLY386 4.4 99.3 1.0 C44 D:QIY301 4.5 129.6 1.0 O A:GLU383 4.6 84.4 1.0 CB D:PRO99 4.6 88.1 1.0 CZ D:ARG107 4.6 143.4 1.0 NH1 D:ARG107 4.9 130.4 1.0 CD1 D:ILE109 4.9 124.0 1.0 N A:GLY386 4.9 92.0 1.0

Chlorine binding site 3 out of 4 in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 48


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex Between Vcb, BRD4-BD2 and Protac 48 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:111.4 occ:1.00 CL30 H:QIY301 0.0 111.4 1.0 C29 H:QIY301 1.7 100.2 1.0 C31 H:QIY301 2.7 96.5 1.0 C28 H:QIY301 2.7 95.7 1.0 OE2 E:GLU438 3.3 132.2 1.0 CD E:GLU438 3.4 118.2 1.0 OE1 E:GLU438 3.6 113.9 1.0 C32 H:QIY301 4.0 93.5 1.0 C27 H:QIY301 4.0 90.9 1.0 SD E:MET442 4.0 101.2 1.0 CB E:GLU438 4.2 110.2 1.0 CG E:GLU438 4.3 115.2 1.0 NH1 H:ARG69 4.3 113.8 1.0 NH2 H:ARG69 4.3 135.7 1.0 C63 H:QIY301 4.4 108.2 1.0 CE E:MET442 4.4 106.3 1.0 C26 H:QIY301 4.5 93.1 1.0 CZ2 E:TRP374 4.6 81.1 1.0 CZ H:ARG69 4.7 137.0 1.0 CH2 E:TRP374 4.9 79.4 1.0

Chlorine binding site 4 out of 4 in the Ternary Complex Between Vcb, BRD4-BD2 and Protac 48


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex Between Vcb, BRD4-BD2 and Protac 48 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:159.2 occ:1.00 CL38 H:QIY301 0.0 159.2 1.0 C39 H:QIY301 1.7 121.7 1.0 C40 H:QIY301 2.7 125.7 1.0 C42 H:QIY301 2.7 111.0 1.0 CG H:PRO99 3.8 87.6 1.0 CD H:PRO99 3.9 97.0 1.0 C41 H:QIY301 4.0 116.6 1.0 CA E:GLY386 4.0 99.0 1.0 C43 H:QIY301 4.0 105.3 1.0 N E:GLY386 4.5 99.8 1.0 C44 H:QIY301 4.5 110.9 1.0 CB H:PRO99 4.6 94.7 1.0 CD H:ARG107 4.7 118.2 1.0 NH1 H:ARG107 4.8 121.5 1.0 O E:GLU383 4.9 89.8 1.0 C E:LEU385 5.0 99.7 1.0 CD1 H:ILE109 5.0 108.9 1.0 O E:LEU385 5.0 90.0 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