Fluorine in PDB 8qtk: Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)

The structure of Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31), PDB code: 8qtk was solved by M.Schimpl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.48 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.268, 74.966, 97.56, 90, 90, 90
R / Rfree (%)	20.9 / 26.8

The structure of Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) (pdb code 8qtk). 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 Cbl-B in Complex with An Allosteric Inhibitor (Compound 31), PDB code: 8qtk:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)


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 Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:35.7 occ:1.00 F2 A:WX9504 0.0 35.7 1.0 C19 A:WX9504 1.3 35.9 1.0 F1 A:WX9504 2.1 36.2 1.0 F A:WX9504 2.1 37.7 1.0 C17 A:WX9504 2.3 34.3 1.0 C18 A:WX9504 3.0 32.9 1.0 O A:ARG141 3.1 41.1 1.0 CG A:LYS145 3.2 33.8 1.0 C16 A:WX9504 3.3 34.3 1.0 CB A:THR144 3.4 36.8 1.0 CG2 A:THR144 3.4 35.8 1.0 N A:LYS145 3.5 34.4 1.0 C A:THR144 3.9 35.6 1.0 CG A:ARG141 4.0 46.5 1.0 C A:ARG141 4.0 41.2 1.0 CA A:LYS145 4.0 33.4 1.0 CB A:LYS145 4.2 33.1 1.0 CA A:THR144 4.2 36.3 1.0 C14 A:WX9504 4.3 31.9 1.0 CE A:LYS145 4.3 34.0 1.0 CD A:LYS145 4.4 35.9 1.0 OG1 A:THR144 4.4 37.6 1.0 CA A:ARG141 4.5 41.9 1.0 N3 A:WX9504 4.5 34.5 1.0 O A:THR144 4.6 36.4 1.0 CB A:ARG141 4.8 43.4 1.0 O A:HOH669 4.8 47.0 1.0 O A:MET366 4.8 34.5 1.0 N A:THR144 4.9 36.6 1.0 CD1 A:LEU148 4.9 34.2 1.0 C15 A:WX9504 4.9 33.6 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)


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 Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:37.7 occ:1.00 F A:WX9504 0.0 37.7 1.0 C19 A:WX9504 1.3 35.9 1.0 F1 A:WX9504 2.1 36.2 1.0 F2 A:WX9504 2.1 35.7 1.0 C17 A:WX9504 2.3 34.3 1.0 C18 A:WX9504 2.8 32.9 1.0 C16 A:WX9504 3.5 34.3 1.0 CG A:ARG141 3.5 46.5 1.0 NE A:ARG141 3.5 53.8 1.0 CZ A:ARG141 3.5 55.5 1.0 CE A:LYS145 3.6 34.0 1.0 NH2 A:ARG141 3.7 55.5 1.0 CG A:LYS145 3.8 33.8 1.0 CG A:MET366 3.9 38.8 1.0 O A:MET366 3.9 34.5 1.0 CA A:MET366 4.0 35.3 1.0 NH1 A:ARG141 4.0 53.8 1.0 CD A:ARG141 4.1 50.5 1.0 CB A:MET366 4.1 35.8 1.0 C14 A:WX9504 4.2 31.9 1.0 CD A:LYS145 4.3 35.9 1.0 O A:ARG141 4.4 41.1 1.0 C A:MET366 4.4 35.1 1.0 NZ A:LYS145 4.6 31.4 1.0 N3 A:WX9504 4.6 34.5 1.0 CB A:ARG141 4.8 43.4 1.0 SD A:MET366 4.9 40.7 1.0 OE1 A:GLU365 4.9 54.7 1.0 C A:ARG141 5.0 41.2 1.0 C15 A:WX9504 5.0 33.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)


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 Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:36.2 occ:1.00 F1 A:WX9504 0.0 36.2 1.0 C19 A:WX9504 1.3 35.9 1.0 F A:WX9504 2.1 37.7 1.0 F2 A:WX9504 2.1 35.7 1.0 C17 A:WX9504 2.3 34.3 1.0 C16 A:WX9504 2.7 34.3 1.0 NH1 A:ARG141 3.2 53.8 1.0 CZ A:ARG141 3.5 55.5 1.0 CG A:ARG141 3.6 46.5 1.0 C18 A:WX9504 3.6 32.9 1.0 NH2 A:ARG141 3.9 55.5 1.0 NE A:ARG141 3.9 53.8 1.0 O A:HOH669 4.0 47.0 1.0 N3 A:WX9504 4.1 34.5 1.0 CG2 A:THR144 4.2 35.8 1.0 CD A:ARG141 4.3 50.5 1.0 CB A:THR144 4.3 36.8 1.0 O A:ARG141 4.3 41.1 1.0 CA A:ARG141 4.7 41.9 1.0 CB A:ARG141 4.7 43.4 1.0 C14 A:WX9504 4.7 31.9 1.0 C23 A:WX9504 4.8 38.1 1.0 OG1 A:THR144 4.8 37.6 1.0 O A:HOH651 4.9 62.2 1.0 C A:ARG141 4.9 41.2 1.0 CG A:MET366 5.0 38.8 1.0 C20 A:WX9504 5.0 35.7 1.0 C15 A:WX9504 5.0 33.6 1.0

A.M.Mfuh, J.A.Boerth, G.Bommakanti, C.Chan, A.J.Chinn, E.Code, P.J.Fricke, K.A.Giblin, A.Gohlke, C.Hansel, N.Hariparsad, S.J.Hughes, M.Jin, V.Kantae, S.L.Kavanagh, M.L.Lamb, J.Lane, R.Moore, T.Puri, T.R.Quinn, I.Reddy, G.R.Robb, K.J.Robbins, M.Gancedo Rodrigo, M.Schimpl, B.Singh, M.Singh, H.Tang, C.Thomson, J.J.Walsh, J.Ware, I.D.G.Watson, M.W.Ye, G.L.Wrigley, A.X.Zhang, Y.Zhang, N.P.Grimster. Discovery, Optimization, and Biological Evaluation of Arylpyridones As Cbl-B Inhibitors. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38227216
DOI: 10.1021/ACS.JMEDCHEM.3C02083