Fluorine in PDB 6tom: Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1

The structure of Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1, PDB code: 6tom was solved by M.J.Rodrigues, Y.-V.Le Bihan, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.42 / 1.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.279, 67.279, 166.379, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 21.8

The structure of Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1 (pdb code 6tom). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1, PDB code: 6tom:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:78.7 occ:0.75 F A:NQZ201 0.0 78.7 0.8 C6 A:NQZ201 1.4 77.6 0.8 F1 A:NQZ201 2.2 79.6 0.8 C4 A:NQZ201 2.4 75.6 0.8 C1 A:NQZ201 2.4 76.2 0.8 C5 A:NQZ201 2.8 75.9 0.8 C A:NQZ201 2.8 76.9 0.8 C2 A:NQZ201 2.9 74.4 0.8 C3 A:NQZ201 3.0 74.3 0.8 N A:NQZ201 3.5 72.3 0.8 C7 A:NQZ201 4.8 66.5 0.8

Fluorine binding site 2 out of 2 in the Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human BCL6 Btb Domain in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:79.6 occ:0.75 F1 A:NQZ201 0.0 79.6 0.8 C6 A:NQZ201 1.4 77.6 0.8 F A:NQZ201 2.2 78.7 0.8 C1 A:NQZ201 2.4 76.2 0.8 C4 A:NQZ201 2.4 75.6 0.8 C A:NQZ201 3.0 76.9 0.8 C5 A:NQZ201 3.0 75.9 0.8 C2 A:NQZ201 3.7 74.4 0.8 C3 A:NQZ201 3.7 74.3 0.8 N A:NQZ201 4.1 72.3 0.8 CE2 A:TYR58 4.1 45.0 1.0 OH A:TYR58 4.6 54.7 1.0 CZ A:TYR58 4.7 52.2 1.0 CD2 A:TYR58 4.8 43.6 1.0

B.R.Bellenie, K.J.Cheung, A.Varela, O.A.Pierrat, G.W.Collie, G.M.Box, M.D.Bright, S.Gowan, A.Hayes, M.J.Rodrigues, K.N.Shetty, M.Carter, O.A.Davis, A.T.Henley, P.Innocenti, L.D.Johnson, M.Liu, S.De Klerk, Y.V.Le Bihan, M.G.Lloyd, P.C.Mcandrew, E.Shehu, R.Talbot, H.L.Woodward, R.Burke, V.Kirkin, R.L.M.Van Montfort, F.I.Raynaud, O.W.Rossanese, S.Hoelder. Achievingin Vivotarget Depletion Through the Discovery and Optimization of Benzimidazolone BCL6 Degraders. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32275432
DOI: 10.1021/ACS.JMEDCHEM.9B02076