Chlorine in PDB 8bdj: Vcb in Complex with Compound 30

The structure of Vcb in Complex with Compound 30, PDB code: 8bdj 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)	91.33 / 2.02
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.334, 93.334, 365.296, 90, 90, 90
R / Rfree (%)	19.4 / 23.9

The structure of Vcb in Complex with Compound 30 also contains other interesting chemical elements:

Arsenic

(As)

5 atoms

The binding sites of Chlorine atom in the Vcb in Complex with Compound 30 (pdb code 8bdj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Vcb in Complex with Compound 30, PDB code: 8bdj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:91.4 occ:1.00 CL30 C:QE0301 0.0 91.4 1.0 C27 C:QE0301 1.7 65.7 1.0 C28 C:QE0301 2.7 58.3 1.0 C26 C:QE0301 2.7 56.4 1.0 O C:HOH430 3.0 56.4 1.0 O C:HOH441 3.2 53.4 1.0 CD C:PRO99 3.6 39.8 1.0 C25 C:QE0301 4.0 58.6 1.0 C29 C:QE0301 4.0 55.0 1.0 CD2 C:TYR98 4.0 39.3 1.0 CG C:PRO99 4.1 39.9 1.0 NE C:ARG107 4.1 71.6 1.0 CG2 C:ILE109 4.4 52.2 1.0 C24 C:QE0301 4.5 56.8 1.0 CB C:PRO99 4.5 41.1 1.0 NH2 C:ARG107 4.6 71.7 1.0 N C:PRO99 4.6 37.5 1.0 CB C:TYR98 4.6 36.3 1.0 CG C:TYR98 4.8 36.0 1.0 CZ C:ARG107 4.8 70.7 1.0 CE2 C:TYR98 4.8 37.8 1.0 CD C:ARG107 4.8 65.7 1.0

Chlorine binding site 2 out of 4 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl301 b:130.0 occ:1.00 CL30 F:QE0301 0.0 130.0 1.0 C27 F:QE0301 1.7 81.7 1.0 C26 F:QE0301 2.7 67.7 1.0 C28 F:QE0301 2.7 77.0 1.0 O F:HOH432 2.7 56.6 1.0 O F:HOH436 3.3 59.0 1.0 CD F:PRO99 3.4 43.2 1.0 NE F:ARG107 3.7 67.2 1.0 CG F:PRO99 4.0 43.7 1.0 C25 F:QE0301 4.0 68.3 1.0 C29 F:QE0301 4.0 72.5 1.0 CD2 F:TYR98 4.0 43.5 1.0 NH2 F:ARG107 4.3 71.1 1.0 CG2 F:ILE109 4.3 54.1 1.0 CB F:PRO99 4.4 44.7 1.0 N F:PRO99 4.4 41.0 1.0 CZ F:ARG107 4.5 69.7 1.0 C24 F:QE0301 4.5 66.5 1.0 CD F:ARG107 4.5 65.2 1.0 CB F:TYR98 4.5 40.4 1.0 CG F:TYR98 4.8 40.0 1.0 O F:PRO99 4.9 39.3 1.0 CE2 F:TYR98 4.9 45.0 1.0 CG F:ARG107 5.0 59.8 1.0

Chlorine binding site 3 out of 4 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl301 b:89.9 occ:1.00 CL30 I:QE0301 0.0 89.9 1.0 C27 I:QE0301 1.8 67.8 1.0 C26 I:QE0301 2.7 64.1 1.0 C28 I:QE0301 2.7 62.7 1.0 NH2 I:ARG107 3.5 73.3 1.0 CG2 I:ILE109 3.7 47.5 1.0 CD I:PRO99 3.8 45.1 1.0 NE I:ARG107 3.9 69.3 1.0 C25 I:QE0301 4.0 59.0 1.0 C29 I:QE0301 4.0 59.0 1.0 CZ I:ARG107 4.0 73.9 1.0 CB I:TYR98 4.2 42.8 1.0 CD2 I:TYR98 4.2 42.2 1.0 CE2 I:PHE76 4.3 42.8 1.0 O I:PRO99 4.4 40.9 1.0 N I:PRO99 4.4 43.8 1.0 CG I:PRO99 4.4 46.9 1.0 CD2 I:PHE76 4.5 41.6 1.0 CB I:ILE109 4.5 45.9 1.0 C24 I:QE0301 4.5 57.4 1.0 CG I:TYR98 4.6 42.2 1.0 CB I:PRO99 4.7 45.9 1.0

Chlorine binding site 4 out of 4 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl301 b:88.9 occ:1.00 CL30 L:QE0301 0.0 88.9 1.0 C27 L:QE0301 1.8 56.2 1.0 C26 L:QE0301 2.7 52.3 1.0 C28 L:QE0301 2.7 52.9 1.0 O L:HOH444 3.3 59.5 1.0 NH1 L:ARG107 3.5 58.1 1.0 CG2 L:ILE109 3.7 44.2 1.0 CD L:PRO99 3.8 40.5 1.0 CZ L:ARG107 4.0 63.2 1.0 C25 L:QE0301 4.0 53.1 1.0 C29 L:QE0301 4.0 47.8 1.0 CD L:ARG107 4.2 54.7 1.0 CB L:TYR98 4.3 36.9 1.0 NE L:ARG107 4.3 60.0 1.0 CD2 L:TYR98 4.3 37.1 1.0 CE2 L:PHE76 4.3 35.0 1.0 O L:PRO99 4.4 36.9 1.0 N L:PRO99 4.4 38.8 1.0 CD2 L:PHE76 4.5 36.1 1.0 C24 L:QE0301 4.5 51.7 1.0 CB L:ILE109 4.5 43.4 1.0 CG L:PRO99 4.6 41.0 1.0 CB L:PRO99 4.7 40.3 1.0 CG L:TYR98 4.7 37.8 1.0 NH2 L:ARG107 4.8 65.5 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