Arsenic 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:

Chlorine

(Cl)

4 atoms

The binding sites of Arsenic atom in the Vcb in Complex with Compound 30 (pdb code 8bdj). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 5 binding sites of Arsenic where determined in the Vcb in Complex with Compound 30, PDB code: 8bdj:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5;

Arsenic binding site 1 out of 5 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:89.4 occ:1.00 AS C:CAS77 0.0 89.4 1.0 CE1 C:CAS77 2.0 79.5 1.0 CE2 C:CAS77 2.0 87.0 1.0 SG C:CAS77 2.2 73.1 1.0 CB C:CAS77 3.2 60.5 1.0 CA C:CAS77 3.6 51.0 1.0 CA C:GLY106 4.0 50.3 1.0 N C:GLY106 4.1 51.2 1.0 O C:THR105 4.2 48.0 1.0 C C:THR105 4.2 51.4 1.0 C C:CAS77 4.3 47.9 1.0 N C:ASN78 4.5 45.9 1.0 CE2 C:PHE148 4.7 76.3 1.0 N C:CAS77 4.8 48.1 1.0 NE C:ARG79 4.9 74.9 1.0 O C:PHE76 5.0 49.8 1.0

Arsenic binding site 2 out of 5 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:84.9 occ:1.00 AS F:CAS77 0.0 84.9 1.0 CE1 F:CAS77 2.0 82.0 1.0 CE2 F:CAS77 2.0 84.7 1.0 SG F:CAS77 2.3 69.5 1.0 CB F:CAS77 3.3 56.3 1.0 CA F:CAS77 3.6 51.2 1.0 CA F:GLY106 3.9 59.1 1.0 N F:GLY106 4.1 62.9 1.0 C F:THR105 4.2 46.7 1.0 O F:THR105 4.2 45.8 1.0 C F:CAS77 4.4 49.9 1.0 N F:ASN78 4.5 45.8 1.0 CZ H:PHE109 4.7 64.7 1.0 CE2 F:PHE148 4.7 69.5 1.0 CE H:MET45 4.8 84.0 1.0 N F:CAS77 4.9 48.4 1.0 O F:PHE76 4.9 50.1 1.0

Arsenic binding site 3 out of 5 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:75.6 occ:1.00 AS I:CAS77 0.0 75.6 1.0 CE2 I:CAS77 2.0 76.2 1.0 CE1 I:CAS77 2.0 74.6 1.0 SG I:CAS77 2.3 62.9 1.0 CB I:CAS77 3.3 49.7 1.0 CA I:CAS77 3.5 44.6 1.0 CA I:GLY106 3.8 51.4 1.0 N I:GLY106 4.0 54.0 1.0 O I:THR105 4.1 46.9 1.0 C I:THR105 4.2 49.6 1.0 C I:CAS77 4.2 43.0 1.0 N I:ASN78 4.3 42.2 1.0 N I:CAS77 4.8 41.6 1.0 CE2 I:PHE148 4.8 60.6 1.0 O I:PHE76 4.9 42.7 1.0

Arsenic binding site 4 out of 5 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ J:As89 b:144.0 occ:1.00 AS J:CAS89 0.0 144.0 1.0 CE1 J:CAS89 2.0 135.9 1.0 CE2 J:CAS89 2.0 126.3 1.0 SG J:CAS89 2.3 83.5 1.0 CB J:CAS89 3.4 66.4 1.0 OE2 J:GLU91 4.2 57.3 1.0 CA J:CAS89 4.5 58.3 1.0 O A:HOH247 4.8 60.6 1.0

Arsenic binding site 5 out of 5 in the Vcb in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Vcb in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ L:As77 b:64.8 occ:1.00 AS L:CAS77 0.0 64.8 1.0 CE1 L:CAS77 2.0 64.0 1.0 CE2 L:CAS77 2.0 65.5 1.0 SG L:CAS77 2.2 49.4 1.0 CB L:CAS77 3.2 41.8 1.0 CA L:CAS77 3.5 36.9 1.0 CA L:GLY106 3.9 40.8 1.0 O L:THR105 4.0 37.4 1.0 N L:GLY106 4.1 40.6 1.0 C L:CAS77 4.1 35.9 1.0 C L:THR105 4.1 39.8 1.0 N L:ASN78 4.3 35.2 1.0 CE2 L:PHE148 4.8 45.9 1.0 N L:CAS77 4.8 35.1 1.0 O L:PHE76 5.0 37.6 1.0 O L:CAS77 5.0 33.7 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