Fluorine in PDB 8pqg: C-Kit T670I Mutated Kinase Domain in Complex with Avapritinib

All present enzymatic activity of C-Kit T670I Mutated Kinase Domain in Complex with Avapritinib:
2.7.10.1;

The structure of C-Kit T670I Mutated Kinase Domain in Complex with Avapritinib, PDB code: 8pqg 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)	48.10 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.75, 59.09, 192.42, 90, 90, 90
R / Rfree (%)	20.6 / 23.1

The binding sites of Fluorine atom in the C-Kit T670I Mutated Kinase Domain in Complex with Avapritinib (pdb code 8pqg). 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 T670I Mutated Kinase Domain in Complex with Avapritinib, PDB code: 8pqg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the C-Kit T670I Mutated 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 T670I Mutated Kinase Domain in Complex with Avapritinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:68.0 occ:1.00 F A:9JI1001 0.0 68.0 1.0 C17 A:9JI1001 1.4 66.4 1.0 C16 A:9JI1001 2.3 64.2 1.0 C18 A:9JI1001 2.3 62.9 1.0 O A:MET624 3.0 66.0 1.0 CD2 A:LEU625 3.1 76.4 1.0 C A:MET624 3.3 67.1 1.0 CG A:LEU625 3.4 72.1 1.0 C15 A:9JI1001 3.6 62.2 1.0 C19 A:9JI1001 3.6 61.5 1.0 CG A:LYS623 3.6 63.3 1.0 N A:LEU625 3.7 69.3 1.0 N A:MET624 3.8 65.2 1.0 CE A:LYS623 3.9 62.9 1.0 CA A:MET624 4.0 66.1 1.0 CD1 A:LEU637 4.0 62.4 1.0 CA A:LEU625 4.0 71.8 1.0 C14 A:9JI1001 4.1 62.6 1.0 CD2 A:LEU637 4.2 60.1 1.0 CB A:LEU625 4.3 70.5 1.0 C A:LYS623 4.4 62.0 1.0 CD A:LYS623 4.4 62.9 1.0 CA A:GLY601 4.5 76.2 1.0 CG A:LEU637 4.6 62.1 1.0 CD1 A:LEU625 4.6 72.3 1.0 O A:LYS602 4.7 64.4 1.0 N A:LYS602 4.7 65.6 1.0 CB A:LYS623 4.8 60.3 1.0 O A:LYS623 4.9 62.0 1.0 C A:GLY601 4.9 71.0 1.0 CB A:LEU637 5.0 64.7 1.0 N A:GLY601 5.0 80.6 1.0

Fluorine binding site 2 out of 2 in the C-Kit T670I Mutated 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 T670I Mutated Kinase Domain in Complex with Avapritinib within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:57.3 occ:1.00 F C:9JI1001 0.0 57.3 1.0 C17 C:9JI1001 1.4 58.9 1.0 C16 C:9JI1001 2.3 58.8 1.0 C18 C:9JI1001 2.3 54.5 1.0 O C:MET624 3.4 61.1 1.0 CG C:LEU625 3.4 62.9 1.0 CD2 C:LEU625 3.5 65.4 1.0 C15 C:9JI1001 3.6 59.0 1.0 C19 C:9JI1001 3.6 58.8 1.0 CD1 C:LEU637 3.7 57.3 1.0 C C:MET624 3.7 59.3 1.0 CE C:LYS623 3.9 56.0 1.0 CG C:LYS623 3.9 56.5 1.0 CD2 C:LEU637 4.0 58.4 1.0 C14 C:9JI1001 4.1 59.9 1.0 N C:LEU625 4.2 60.5 1.0 CG C:LEU637 4.2 59.2 1.0 CA C:LEU625 4.3 62.6 1.0 CD1 C:LEU625 4.3 63.0 1.0 N C:MET624 4.4 58.8 1.0 CB C:LEU637 4.4 60.0 1.0 CB C:LEU625 4.4 63.8 1.0 CA C:MET624 4.5 60.4 1.0 CA C:GLY601 4.5 64.6 1.0 CD C:LYS623 4.5 57.7 1.0 C C:LYS623 4.9 59.1 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