Fluorine in PDB 6gqm: Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229

All present enzymatic activity of Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229:
2.7.10.1;

The structure of Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229, PDB code: 6gqm was solved by M.Schimpl, C.J.Hardy, D.J.Ogg, R.C.Overman, M.J.Packer, J.G.Kettle, R.Anjum, E.Barry, D.Bhavsar, C.Brown, A.Campbell, K.Goldberg, M.Grondine, S.Guichard, T.Hunt, O.Jones, X.Li, O.Moleva, S.Pearson, W.Shao, A.Smith, J.Smith, D.Stead, S.Stokes, M.Tucker, Y.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.970, 90.180, 91.150, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23

The structure of Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229 (pdb code 6gqm). 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 C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229, PDB code: 6gqm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229


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 C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:37.8 occ:1.00 F A:F8H1001 0.0 37.8 1.0 C19 A:F8H1001 1.3 34.6 1.0 C18 A:F8H1001 2.3 35.3 1.0 C14 A:F8H1001 2.4 34.5 1.0 N4 A:F8H1001 2.7 31.2 1.0 C13 A:F8H1001 3.0 31.8 1.0 CE2 A:PHE811 3.1 33.7 1.0 CZ A:PHE811 3.1 30.9 1.0 CB A:LEU595 3.6 37.6 1.0 C17 A:F8H1001 3.6 36.1 1.0 C15 A:F8H1001 3.6 33.7 1.0 O A:HOH1166 3.7 44.3 1.0 O A:LEU595 3.8 37.8 1.0 C10 A:F8H1001 4.0 28.7 1.0 C16 A:F8H1001 4.1 36.6 1.0 C A:LEU595 4.1 39.9 1.0 O A:HOH1127 4.1 39.7 1.0 N6 A:F8H1001 4.3 32.7 1.0 CD2 A:PHE811 4.4 31.8 1.0 CD1 A:LEU595 4.4 42.9 1.0 CE1 A:PHE811 4.4 32.0 1.0 CA A:LEU595 4.5 37.8 1.0 C11 A:F8H1001 4.6 25.4 1.0 CG A:LEU595 4.6 43.1 1.0 O1 A:F8H1001 4.6 35.9 1.0 CD2 A:LEU799 4.7 35.3 1.0 CG1 A:VAL603 4.7 35.5 1.0 N A:GLY596 4.8 34.7 1.0 N5 A:F8H1001 4.8 34.1 1.0 C23 A:F8H1001 5.0 29.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229


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 C-Kit Kinase Domain in Complex with A Small Molecule Inhibitor, AZD3229 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:44.7 occ:1.00 F B:F8H1001 0.0 44.7 1.0 C19 B:F8H1001 1.4 43.1 1.0 C18 B:F8H1001 2.3 41.0 1.0 C14 B:F8H1001 2.4 41.2 1.0 N4 B:F8H1001 2.7 40.6 1.0 C13 B:F8H1001 3.0 40.6 1.0 CE2 B:PHE811 3.0 44.1 1.0 CZ B:PHE811 3.1 41.9 1.0 CB B:LEU595 3.6 53.9 1.0 C17 B:F8H1001 3.6 41.1 1.0 C15 B:F8H1001 3.7 40.3 1.0 O B:LEU595 3.8 57.0 1.0 C10 B:F8H1001 4.0 38.6 1.0 O B:HOH1161 4.0 43.8 1.0 C16 B:F8H1001 4.1 39.7 1.0 C B:LEU595 4.2 57.0 1.0 N6 B:F8H1001 4.3 39.9 1.0 CD2 B:PHE811 4.3 41.1 1.0 CD1 B:LEU595 4.4 58.9 1.0 CE1 B:PHE811 4.4 41.6 1.0 CA B:LEU595 4.5 55.0 1.0 C11 B:F8H1001 4.5 38.0 1.0 CG B:LEU595 4.5 60.1 1.0 CD2 B:LEU799 4.6 44.5 1.0 CG1 B:VAL603 4.6 48.7 1.0 O1 B:F8H1001 4.7 45.6 1.0 N B:GLY596 4.8 52.6 1.0 N5 B:F8H1001 4.8 39.9 1.0 C23 B:F8H1001 5.0 38.9 1.0

J.G.Kettle, R.Anjum, E.Barry, D.Bhavsar, C.Brown, S.Boyd, A.Campbell, K.Goldberg, M.Grondine, S.Guichard, C.J.Hardy, T.Hunt, R.D.O.Jones, X.Li, O.Moleva, D.Ogg, R.C.Overman, M.J.Packer, S.Pearson, M.Schimpl, W.Shao, A.Smith, J.M.Smith, D.Stead, S.Stokes, M.Tucker, Y.Ye. Discovery of N-(4-{[5-Fluoro-7-(2-Methoxyethoxy) Quinazolin-4-Yl]Amino}Phenyl)-2-[4-(Propan-2-Yl)-1 H-1,2,3-Triazol-1-Yl]Acetamide (AZD3229), A Potent Pan-Kit Mutant Inhibitor For the Treatment of Gastrointestinal Stromal Tumors. J. Med. Chem. V. 61 8797 2018.
ISSN: ISSN 1520-4804
PubMed: 30204441
DOI: 10.1021/ACS.JMEDCHEM.8B00938