Fluorine in PDB 8pq9: C-Kit Kinase Domain in Complex with Avapritinib

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

The structure of C-Kit Kinase Domain in Complex with Avapritinib, PDB code: 8pq9 was solved by A.Teuber, S.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)	35.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.02, 59.3, 191.76, 90, 90, 90
R / Rfree (%)	19.1 / 20.4

The binding sites of Fluorine atom in the C-Kit Kinase Domain in Complex with Avapritinib (pdb code 8pq9). 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, PDB code: 8pq9:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:41.5 occ:1.00 F A:9JI1001 0.0 41.5 1.0 C17 A:9JI1001 1.4 35.7 1.0 C16 A:9JI1001 2.3 36.1 1.0 C18 A:9JI1001 2.4 37.5 1.0 CD2 A:LEU625 3.1 48.6 1.0 O A:MET624 3.3 38.6 1.0 CG A:LEU625 3.5 41.8 1.0 C A:MET624 3.5 40.5 1.0 C15 A:9JI1001 3.6 35.6 1.0 C19 A:9JI1001 3.6 38.8 1.0 N A:LEU625 3.8 42.7 1.0 CG A:LYS623 3.8 29.4 1.0 CE A:LYS623 4.0 34.1 1.0 CA A:LEU625 4.0 49.2 1.0 C14 A:9JI1001 4.1 37.8 1.0 N A:MET624 4.1 33.7 1.0 CD1 A:LEU637 4.2 35.0 1.0 CD2 A:LEU637 4.2 35.5 1.0 CA A:MET624 4.3 37.5 1.0 CB A:LEU625 4.3 48.0 1.0 CA A:GLY601 4.5 48.8 1.0 CD A:LYS623 4.5 30.3 1.0 CG A:LEU637 4.7 34.2 1.0 CD1 A:LEU625 4.7 45.2 1.0 C A:LYS623 4.8 34.7 1.0 N A:LYS602 4.9 39.8 1.0 N A:GLY601 4.9 53.2 1.0 CB A:LEU637 4.9 39.0 1.0 O A:PHE600 4.9 76.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:37.4 occ:1.00 F C:9JI1001 0.0 37.4 1.0 C17 C:9JI1001 1.4 37.8 1.0 C16 C:9JI1001 2.3 34.8 1.0 C18 C:9JI1001 2.3 38.5 1.0 CD2 C:LEU625 3.1 41.1 1.0 O C:MET624 3.4 33.5 1.0 CG C:LEU625 3.5 37.8 1.0 C15 C:9JI1001 3.6 35.9 1.0 C19 C:9JI1001 3.6 36.1 1.0 C C:MET624 3.6 31.9 1.0 CG C:LYS623 3.8 28.3 1.0 CE C:LYS623 3.8 31.5 1.0 CD1 C:LEU637 4.0 31.9 1.0 N C:LEU625 4.0 37.1 1.0 O C:HOH1246 4.1 41.0 1.0 CD2 C:LEU637 4.1 32.0 1.0 C14 C:9JI1001 4.1 35.5 1.0 N C:MET624 4.2 30.2 1.0 CA C:LEU625 4.2 38.9 1.0 CA C:MET624 4.3 32.4 1.0 CD C:LYS623 4.4 30.4 1.0 CG C:LEU637 4.4 31.8 1.0 CA C:GLY601 4.4 41.5 1.0 CB C:LEU625 4.5 42.2 1.0 CD1 C:LEU625 4.6 42.6 1.0 CB C:LEU637 4.7 33.5 1.0 C C:LYS623 4.8 30.9 1.0 N C:LYS602 4.9 34.3 1.0 O C:LYS602 4.9 35.4 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