Fluorine in PDB 5x4o: Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5, PDB code: 5x4o was solved by S.Sogabe, K.Ida, W.Lane, G.Snell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.05
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.439, 66.439, 152.797, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.3

The binding sites of Fluorine atom in the Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5 (pdb code 5x4o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5, PDB code: 5x4o:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5


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 the BCL6 Btb Domain in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:62.2 occ:1.00 F29 A:YAM801 0.0 62.2 1.0 C8 A:YAM801 1.4 64.3 1.0 F27 A:YAM801 2.1 64.2 1.0 F28 A:YAM801 2.2 69.3 1.0 C6 A:YAM801 2.4 61.3 1.0 C7 A:YAM801 2.8 57.3 1.0 CB A:ARG24 3.3 47.9 1.0 CD A:ARG28 3.6 57.9 1.0 C A:ARG24 3.6 44.5 1.0 CD2 A:LEU25 3.6 43.8 1.0 N A:LEU25 3.6 43.1 1.0 C5 A:YAM801 3.7 62.5 1.0 O A:ARG24 3.9 44.5 1.0 NE A:ARG28 3.9 63.2 1.0 CA A:ARG24 4.1 44.6 1.0 CA A:LEU25 4.1 42.4 1.0 N2 A:YAM801 4.2 55.8 1.0 N10 A:YAM801 4.2 66.7 1.0 CZ A:ARG28 4.2 66.6 1.0 O A:ASN21 4.2 37.1 1.0 NH2 A:ARG28 4.3 65.8 1.0 CG A:LEU25 4.3 42.8 1.0 CD A:ARG24 4.5 55.3 1.0 CG A:ARG24 4.5 51.0 1.0 CD1 A:ILE30 4.7 48.6 1.0 CB A:LEU25 4.8 42.0 1.0 N4 A:YAM801 4.8 58.3 1.0 CG A:ARG28 4.9 54.7 1.0 C3 A:YAM801 4.9 57.6 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5


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 the BCL6 Btb Domain in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:69.3 occ:1.00 F28 A:YAM801 0.0 69.3 1.0 C8 A:YAM801 1.4 64.3 1.0 F27 A:YAM801 2.1 64.2 1.0 F29 A:YAM801 2.2 62.2 1.0 C6 A:YAM801 2.4 61.3 1.0 N10 A:YAM801 2.9 66.7 1.0 C5 A:YAM801 3.0 62.5 1.0 CD A:ARG24 3.1 55.3 1.0 CB A:ARG24 3.2 47.9 1.0 C7 A:YAM801 3.5 57.3 1.0 CG A:ARG24 3.7 51.0 1.0 CZ A:ARG28 3.7 66.6 1.0 NE A:ARG28 3.8 63.2 1.0 NH1 A:ARG28 3.9 68.8 1.0 NH2 A:ARG28 4.0 65.8 1.0 NE A:ARG24 4.2 59.5 1.0 C12 A:YAM801 4.2 71.6 1.0 NH1 A:ARG24 4.2 63.5 1.0 N4 A:YAM801 4.3 58.3 1.0 CD A:ARG28 4.3 57.9 1.0 CA A:ARG24 4.6 44.6 1.0 CZ A:ARG24 4.6 61.0 1.0 N2 A:YAM801 4.7 55.8 1.0 C A:ARG24 4.8 44.5 1.0 C3 A:YAM801 5.0 57.6 1.0 OD1 A:ASN21 5.0 42.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the BCL6 Btb Domain in Complex with Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:64.2 occ:1.00 F27 A:YAM801 0.0 64.2 1.0 C8 A:YAM801 1.4 64.3 1.0 F29 A:YAM801 2.1 62.2 1.0 F28 A:YAM801 2.1 69.3 1.0 C6 A:YAM801 2.4 61.3 1.0 N10 A:YAM801 3.0 66.7 1.0 C5 A:YAM801 3.0 62.5 1.0 C7 A:YAM801 3.4 57.3 1.0 NE A:ARG28 3.6 63.2 1.0 CD A:ARG28 3.8 57.9 1.0 CZ A:ARG28 4.1 66.6 1.0 N4 A:YAM801 4.2 58.3 1.0 C12 A:YAM801 4.3 71.6 1.0 N2 A:YAM801 4.6 55.8 1.0 NH1 A:ARG28 4.6 68.8 1.0 C17 A:YAM801 4.6 76.2 1.0 CB A:ARG24 4.8 47.9 1.0 NH2 A:ARG28 4.8 65.8 1.0 C3 A:YAM801 4.8 57.6 1.0

Y.Kamada, N.Sakai, S.Sogabe, K.Ida, H.Oki, K.Sakamoto, W.Lane, G.Snell, M.Iida, Y.Imaeda, J.Sakamoto, J.Matsui. Discovery of A B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor By A Biophysics-Driven Fragment-Based Approach J. Med. Chem. V. 60 4358 2017.
ISSN: ISSN 1520-4804
PubMed: 28471657
DOI: 10.1021/ACS.JMEDCHEM.7B00313