Fluorine in PDB 8pqd: C-Kit Kinase Domain in Complex with Avapritinib Derivative 10

All present enzymatic activity of C-Kit Kinase Domain in Complex with Avapritinib Derivative 10:
2.7.10.1;

The structure of C-Kit Kinase Domain in Complex with Avapritinib Derivative 10, PDB code: 8pqd was solved by A.Teuber, M.P.Mueller, D.Rauh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.99 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.39, 59.37, 192.89, 90, 90, 90
R / Rfree (%)	17.5 / 19.4

The binding sites of Fluorine atom in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 10 (pdb code 8pqd). 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 10, PDB code: 8pqd:
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 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:26.6 occ:0.69 F35 A:9VV1001 0.0 26.6 0.7 C32 A:9VV1001 1.4 27.7 1.0 C31 A:9VV1001 2.4 25.6 1.0 C33 A:9VV1001 2.4 26.5 0.8 CD2 A:LEU625 3.2 43.0 1.0 O A:MET624 3.4 33.4 1.0 CG A:LEU625 3.4 37.5 1.0 C A:MET624 3.5 32.6 1.0 C30 A:9VV1001 3.6 23.3 1.0 C34 A:9VV1001 3.7 24.3 0.8 CG A:LYS623 3.7 25.3 1.0 N A:LEU625 3.8 30.1 1.0 CE A:LYS623 3.9 29.3 1.0 CA A:LEU625 4.0 34.7 1.0 CD1 A:LEU637 4.0 25.3 1.0 O A:HOH1292 4.1 38.3 1.0 CD2 A:LEU637 4.1 26.7 1.0 N A:MET624 4.1 25.1 1.0 C29 A:9VV1001 4.2 26.2 1.0 CA A:MET624 4.3 26.1 1.0 CB A:LEU625 4.3 32.7 1.0 CD A:LYS623 4.3 26.4 1.0 CG A:LEU637 4.5 24.1 1.0 CD1 A:LEU625 4.6 40.5 1.0 CA A:GLY601 4.7 37.1 1.0 C A:LYS623 4.8 24.9 1.0 CB A:LEU637 4.8 24.9 1.0 O A:PHE600 4.9 53.6 1.0

Fluorine binding site 2 out of 2 in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 10


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 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:31.0 occ:1.00 F35 B:9VV1001 0.0 31.0 1.0 C32 B:9VV1001 1.4 30.1 1.0 C33 B:9VV1001 2.4 26.4 1.0 C31 B:9VV1001 2.4 26.4 1.0 CD2 B:LEU625 3.2 36.7 1.0 CG B:LEU625 3.3 34.8 1.0 O B:MET624 3.4 26.8 1.0 C B:MET624 3.4 24.6 1.0 C34 B:9VV1001 3.6 28.2 1.0 C30 B:9VV1001 3.7 30.0 1.0 CG B:LYS623 3.7 24.2 1.0 N B:LEU625 3.7 28.6 1.0 CE B:LYS623 3.8 24.1 1.0 CD1 B:LEU637 3.9 26.2 1.0 CD2 B:LEU637 3.9 31.4 1.0 N B:MET624 4.0 22.6 1.0 CA B:LEU625 4.0 31.3 1.0 CA B:MET624 4.1 25.0 1.0 O B:HOH1249 4.1 36.8 1.0 C29 B:9VV1001 4.2 27.2 1.0 CB B:LEU625 4.3 31.2 1.0 CD B:LYS623 4.3 25.0 1.0 CG B:LEU637 4.3 25.6 1.0 CD1 B:LEU625 4.4 40.1 1.0 CA B:GLY601 4.5 30.1 1.0 CB B:LEU637 4.6 28.2 1.0 C B:LYS623 4.6 20.7 1.0 CB B:LYS623 4.9 22.8 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