Fluorine in PDB 8pqc: C-Kit Kinase Domain in Complex with Avapritinib Derivative 9

All present enzymatic activity of C-Kit Kinase Domain in Complex with Avapritinib Derivative 9:
2.7.10.1;

The structure of C-Kit Kinase Domain in Complex with Avapritinib Derivative 9, PDB code: 8pqc was solved by A.Teuber, S.B.Kleinboelting, M.P.Mueller, D.Rauh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.53 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.22, 59.22, 192.6, 90, 90, 90
R / Rfree (%)	18.1 / 20.6

The binding sites of Fluorine atom in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 9 (pdb code 8pqc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 9, PDB code: 8pqc:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of C-Kit Kinase Domain in Complex with Avapritinib Derivative 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:28.9 occ:1.00 F31 A:9OO1001 0.0 28.9 1.0 C28 A:9OO1001 1.4 29.5 1.0 C29 A:9OO1001 2.4 24.5 1.0 C27 A:9OO1001 2.4 28.1 1.0 CD2 A:LEU625 3.2 31.9 1.0 O A:MET624 3.3 27.0 1.0 CG A:LEU625 3.4 30.5 1.0 C A:MET624 3.5 26.2 1.0 C30 A:9OO1001 3.6 27.7 1.0 C26 A:9OO1001 3.7 29.8 1.0 CG A:LYS623 3.8 21.9 1.0 N A:LEU625 3.8 27.4 1.0 CE A:LYS623 3.9 26.6 1.0 CD2 A:LEU637 4.0 23.4 1.0 N A:MET624 4.1 23.3 1.0 CA A:LEU625 4.1 31.1 1.0 O A:HOH1178 4.1 29.5 1.0 CD1 A:LEU637 4.1 23.0 1.0 C25 A:9OO1001 4.1 28.5 1.0 CA A:MET624 4.2 25.2 1.0 CA A:GLY601 4.3 32.9 1.0 CB A:LEU625 4.3 29.8 1.0 CD1 A:LEU625 4.4 35.4 1.0 CD A:LYS623 4.5 22.5 1.0 CG A:LEU637 4.5 24.1 1.0 CB A:LEU637 4.7 27.1 1.0 C A:LYS623 4.8 23.4 1.0 N A:LYS602 4.9 28.0 1.0 O A:LYS602 5.0 26.9 1.0

Fluorine binding site 2 out of 2 in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of C-Kit Kinase Domain in Complex with Avapritinib Derivative 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:33.0 occ:1.00 F31 B:9OO1001 0.0 33.0 1.0 C28 B:9OO1001 1.4 31.5 1.0 C29 B:9OO1001 2.4 27.1 1.0 C27 B:9OO1001 2.4 28.5 1.0 CD2 B:LEU625 3.1 38.2 1.0 CG B:LEU625 3.4 36.2 1.0 O B:MET624 3.4 29.6 1.0 C B:MET624 3.5 29.6 1.0 C30 B:9OO1001 3.7 23.6 1.0 C26 B:9OO1001 3.7 26.0 1.0 N B:LEU625 3.8 29.6 1.0 CG B:LYS623 3.8 26.3 1.0 CA B:LEU625 4.0 32.6 1.0 CE B:LYS623 4.0 28.2 1.0 CD1 B:LEU637 4.1 28.8 1.0 C25 B:9OO1001 4.1 27.2 1.0 N B:MET624 4.2 26.5 1.0 O B:HOH1232 4.2 36.6 1.0 CD2 B:LEU637 4.2 28.0 1.0 CB B:LEU625 4.2 33.8 1.0 CA B:MET624 4.3 26.8 1.0 CD B:LYS623 4.4 22.7 1.0 CD1 B:LEU625 4.5 38.6 1.0 CA B:GLY601 4.5 38.6 1.0 CG B:LEU637 4.6 29.4 1.0 C B:LYS623 4.8 27.4 1.0 CB B:LEU637 4.9 29.0 1.0 N B:LYS602 4.9 30.5 1.0 O B:PHE600 4.9 42.2 1.0

A.Teuber, T.Schulz, B.S.Fletcher, R.Gontla, T.Muehlenberg, M.-L.Zischinsky, J.Niggenaber, J.Weisner, S.B.Kleinboelting, J.Lategahn, S.Sievers, M.P.Mueller, S.Bauer, D.Rauh. Avapritinib-Based Sar Studies Reveal A Binding Pocket in Kit and Pdgfra Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-44376-8