Fluorine in PDB 8pqe: C-Kit Kinase Domain in Complex with Avapritinib Derivative 11

All present enzymatic activity of C-Kit Kinase Domain in Complex with Avapritinib Derivative 11:
2.7.10.1;

The structure of C-Kit Kinase Domain in Complex with Avapritinib Derivative 11, PDB code: 8pqe was solved by A.Teuber, J.Niggenaber, M.P.Mueller, D.Rauh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.69 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.97, 62.52, 191.68, 90, 90, 90
R / Rfree (%)	21.4 / 25.6

The structure of C-Kit Kinase Domain in Complex with Avapritinib Derivative 11 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Bromine	(Br)	1 atom

The binding sites of Fluorine atom in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 11 (pdb code 8pqe). 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 11, PDB code: 8pqe:
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 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:79.0 occ:1.00 F33 A:9WU1002 0.0 79.0 1.0 C32 A:9WU1002 1.4 72.8 1.0 C31 A:9WU1002 2.4 70.7 1.0 C34 A:9WU1002 2.4 76.0 1.0 CD2 A:LEU625 3.1 81.6 1.0 O A:MET624 3.3 77.0 1.0 C A:MET624 3.6 73.3 1.0 CG A:LYS623 3.6 58.2 1.0 C30 A:9WU1002 3.6 74.5 1.0 C35 A:9WU1002 3.6 67.9 1.0 CG A:LEU625 3.7 79.1 1.0 N A:LEU625 3.8 68.0 1.0 CA A:LEU625 3.9 77.4 1.0 CD A:LYS623 3.9 72.5 1.0 C29 A:9WU1002 4.1 75.1 1.0 N A:MET624 4.3 66.8 1.0 CD1 A:LEU637 4.4 65.3 1.0 O A:PHE600 4.4 83.0 1.0 CB A:LEU625 4.4 77.8 1.0 CA A:MET624 4.4 71.6 1.0 CD2 A:LEU637 4.6 65.5 1.0 C A:PHE600 4.8 86.4 1.0 CE A:LYS623 4.8 68.2 1.0 CB A:PHE600 4.8 82.8 1.0 CA A:GLY601 4.9 76.0 1.0 C A:LYS623 4.9 66.9 1.0 CG A:LEU637 5.0 59.7 1.0 CD1 A:LEU625 5.0 80.4 1.0

Fluorine binding site 2 out of 2 in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:70.1 occ:1.00 F33 B:9WU1001 0.0 70.1 1.0 C32 B:9WU1001 1.4 62.4 1.0 C31 B:9WU1001 2.4 61.8 1.0 C34 B:9WU1001 2.4 61.0 1.0 CD2 B:LEU625 3.2 66.8 1.0 O B:MET624 3.4 65.9 1.0 CG B:LYS623 3.5 62.7 1.0 C30 B:9WU1001 3.6 62.1 1.0 C B:MET624 3.6 70.2 1.0 C35 B:9WU1001 3.6 61.3 1.0 CG B:LEU625 3.7 74.2 1.0 CD B:LYS623 3.8 71.1 1.0 N B:LEU625 3.8 64.3 1.0 CA B:LEU625 3.9 74.4 1.0 C29 B:9WU1001 4.1 58.5 1.0 CD2 B:LEU637 4.2 52.0 1.0 O B:PHE600 4.2 77.1 1.0 CD1 B:LEU637 4.2 56.0 1.0 N B:MET624 4.3 62.0 1.0 CB B:LEU625 4.3 77.6 1.0 CB B:PHE600 4.4 79.6 1.0 CA B:MET624 4.5 61.4 1.0 C B:PHE600 4.5 74.9 1.0 CG B:LEU637 4.7 55.8 1.0 CE B:LYS623 4.8 65.6 1.0 C B:LYS623 4.8 60.9 1.0 N B:GLY601 4.9 73.9 1.0 CA B:GLY601 4.9 71.7 1.0 CB B:LYS623 4.9 54.8 1.0 O B:HOH1168 5.0 72.1 1.0 CD1 B:LEU625 5.0 72.2 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