Fluorine in PDB 8bdi: Vcb in Complex with Compound 32

The structure of Vcb in Complex with Compound 32, PDB code: 8bdi 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)	91.06 / 2.11
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.733, 92.733, 364.235, 90, 90, 90
R / Rfree (%)	20.8 / 27

The structure of Vcb in Complex with Compound 32 also contains other interesting chemical elements:

Arsenic

(As)

5 atoms

The binding sites of Fluorine atom in the Vcb in Complex with Compound 32 (pdb code 8bdi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Vcb in Complex with Compound 32, PDB code: 8bdi:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Vcb in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Vcb in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ L:F301 b:71.1 occ:1.00 F1 L:QF7301 0.0 71.1 1.0 C15 L:QF7301 1.4 71.2 1.0 C12 L:QF7301 2.4 70.6 1.0 C14 L:QF7301 2.5 71.4 1.0 C13 L:QF7301 2.5 71.4 1.0 N3 L:QF7301 2.6 70.3 1.0 OH L:TYR112 2.9 56.3 1.0 CZ L:TYR112 3.3 53.8 1.0 O4 L:QF7301 3.5 70.1 1.0 CE1 L:TYR112 3.8 52.1 1.0 CE2 L:TYR112 4.0 52.5 1.0 C7 L:QF7301 4.1 70.0 1.0 O3 L:QF7301 4.2 70.3 1.0 C6 L:QF7301 4.5 70.0 1.0 CD1 L:TYR112 4.8 50.7 1.0 C11 L:QF7301 4.8 69.9 1.0 C8 L:QF7301 4.9 69.9 1.0 CD2 L:TYR112 5.0 51.5 1.0

Fluorine binding site 2 out of 4 in the Vcb in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Vcb in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ F:F301 b:81.7 occ:1.00 F1 F:QF7301 0.0 81.7 1.0 C15 F:QF7301 1.4 81.5 1.0 C12 F:QF7301 2.4 81.0 1.0 C13 F:QF7301 2.5 81.6 1.0 C14 F:QF7301 2.5 81.5 1.0 N3 F:QF7301 2.7 80.3 1.0 OH F:TYR112 3.3 60.4 1.0 O4 F:QF7301 3.6 80.9 1.0 CZ F:TYR112 3.8 58.0 1.0 C7 F:QF7301 4.1 79.5 1.0 CE2 F:TYR112 4.4 56.4 1.0 CE1 F:TYR112 4.5 56.8 1.0 O3 F:QF7301 4.6 78.8 1.0 C11 F:QF7301 4.6 79.5 1.0 C8 F:QF7301 4.8 79.3 1.0 C6 F:QF7301 4.8 78.8 1.0 C9 F:QF7301 4.9 79.2 1.0

Fluorine binding site 3 out of 4 in the Vcb in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Vcb in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ I:F301 b:72.5 occ:1.00 F1 I:QF7301 0.0 72.5 1.0 C15 I:QF7301 1.4 72.5 1.0 C12 I:QF7301 2.4 72.2 1.0 C14 I:QF7301 2.5 72.5 1.0 C13 I:QF7301 2.5 72.5 1.0 N3 I:QF7301 2.6 72.1 1.0 OH I:TYR112 3.4 59.2 1.0 O4 I:QF7301 3.6 71.9 1.0 CZ I:TYR112 3.8 56.3 1.0 C7 I:QF7301 4.0 71.7 1.0 CE1 I:TYR112 4.0 54.6 1.0 O3 I:QF7301 4.4 71.7 1.0 C11 I:QF7301 4.5 71.4 1.0 CE2 I:TYR112 4.5 55.0 1.0 C6 I:QF7301 4.7 71.8 1.0 C8 I:QF7301 4.7 71.4 1.0 C9 I:QF7301 4.8 71.4 1.0 CD1 I:TYR112 5.0 53.0 1.0

Fluorine binding site 4 out of 4 in the Vcb in Complex with Compound 32


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Vcb in Complex with Compound 32 within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:67.3 occ:1.00 F1 C:QF7301 0.0 67.3 1.0 C15 C:QF7301 1.4 67.2 1.0 C12 C:QF7301 2.4 66.8 1.0 C13 C:QF7301 2.5 67.1 1.0 C14 C:QF7301 2.5 67.2 1.0 N3 C:QF7301 2.6 66.2 1.0 OH C:TYR112 2.9 53.2 1.0 CZ C:TYR112 3.2 51.2 1.0 O4 C:QF7301 3.5 66.9 1.0 O C:HOH448 3.6 60.6 1.0 CE1 C:TYR112 3.6 50.2 1.0 CE2 C:TYR112 4.0 50.1 1.0 C7 C:QF7301 4.1 65.0 1.0 O3 C:QF7301 4.3 64.4 1.0 C6 C:QF7301 4.5 64.6 1.0 CD1 C:TYR112 4.6 49.0 1.0 C11 C:QF7301 4.7 63.5 1.0 C8 C:QF7301 4.9 64.0 1.0 CD2 C:TYR112 4.9 49.4 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