Chlorine in PDB 8bds: Ternary Complex Between Vcb, BRD4-BD1 and Protac 48

The structure of Ternary Complex Between Vcb, BRD4-BD1 and Protac 48, PDB code: 8bds 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)	68.44 / 1.72
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.031, 79.031, 204.206, 90, 90, 120
R / Rfree (%)	16.8 / 19.7

The binding sites of Chlorine atom in the Ternary Complex Between Vcb, BRD4-BD1 and Protac 48 (pdb code 8bds). 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-BD1 and Protac 48, PDB code: 8bds:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ternary Complex Between Vcb, BRD4-BD1 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-BD1 and Protac 48 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:39.2 occ:1.00 CL30 C:QIY402 0.0 39.2 1.0 C29 C:QIY402 1.8 32.2 1.0 C28 C:QIY402 2.7 28.1 1.0 C31 C:QIY402 2.7 27.7 1.0 C43 C:QIY402 3.4 29.1 1.0 CB D:ASP145 3.4 31.4 1.0 CD2 C:TYR98 3.5 30.9 1.0 CE2 C:TYR98 3.6 30.7 1.0 C44 C:QIY402 4.0 29.2 1.0 SD D:MET149 4.0 33.0 1.0 C27 C:QIY402 4.0 27.7 1.0 C32 C:QIY402 4.0 29.9 1.0 C42 C:QIY402 4.0 28.4 1.0 CD C:PRO99 4.0 31.9 1.0 C45 C:QIY402 4.1 30.5 1.0 CG D:ASP145 4.2 34.6 1.0 CG C:PRO99 4.4 31.8 1.0 OD2 D:ASP145 4.4 37.3 1.0 C26 C:QIY402 4.5 27.4 1.0 O D:HOH631 4.6 31.8 1.0 C46 C:QIY402 4.6 30.4 1.0 N D:ILE146 4.6 25.5 1.0 CG C:TYR98 4.7 29.7 1.0 C D:ASP145 4.7 27.8 1.0 CA D:ASP145 4.7 30.1 1.0 O D:HOH682 4.8 25.8 1.0 CZ C:TYR98 4.9 29.3 1.0 C41 C:QIY402 4.9 29.2 1.0 C39 C:QIY402 5.0 30.1 1.0 O49 C:QIY402 5.0 28.0 1.0

Chlorine binding site 2 out of 2 in the Ternary Complex Between Vcb, BRD4-BD1 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-BD1 and Protac 48 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:35.7 occ:1.00 CL38 C:QIY402 0.0 35.7 1.0 C39 C:QIY402 1.7 30.1 1.0 C42 C:QIY402 2.7 28.4 1.0 C40 C:QIY402 2.7 26.8 1.0 O C:HOH538 3.7 35.1 1.0 NH1 C:ARG107 3.8 34.4 1.0 CE2 C:PHE76 3.9 27.6 1.0 O C:PRO99 3.9 26.5 1.0 CB C:TYR98 3.9 30.5 1.0 CG2 C:ILE109 4.0 35.2 1.0 C43 C:QIY402 4.0 29.1 1.0 C41 C:QIY402 4.0 29.2 1.0 CD2 C:PHE76 4.1 27.5 1.0 CG C:PRO86 4.2 27.2 1.0 CD C:PRO99 4.3 31.9 1.0 CZ C:ARG107 4.3 34.3 1.0 CD C:ARG107 4.3 33.4 1.0 N C:PRO99 4.5 29.9 1.0 NE C:ARG107 4.5 34.8 1.0 C44 C:QIY402 4.6 29.2 1.0 CG C:TYR98 4.7 29.7 1.0 CB C:PRO86 4.7 26.3 1.0 CD2 C:TYR98 4.7 30.9 1.0 C C:TYR98 4.8 30.5 1.0 C C:PRO99 4.8 27.6 1.0 CB C:PRO99 4.8 31.0 1.0 CD1 C:LEU101 4.9 39.6 1.0 CB C:ILE109 4.9 33.3 1.0 CA C:PRO99 5.0 30.1 1.0 CA C:TYR98 5.0 30.1 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