Fluorine in PDB 8pqf: C-Kit Kinase Domain in Complex with Avapritinib Derivative 12

All present enzymatic activity of C-Kit Kinase Domain in Complex with Avapritinib Derivative 12:
2.7.10.1;

The structure of C-Kit Kinase Domain in Complex with Avapritinib Derivative 12, PDB code: 8pqf 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)	43.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.09, 59.25, 191.83, 90, 90, 90
R / Rfree (%)	19.6 / 21.9

The binding sites of Fluorine atom in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 12 (pdb code 8pqf). 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 12, PDB code: 8pqf:
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 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:54.8 occ:1.00 F30 A:9KI1001 0.0 54.8 1.0 C29 A:9KI1001 1.4 44.1 1.0 C31 A:9KI1001 2.4 47.0 1.0 C28 A:9KI1001 2.4 45.8 1.0 CD2 A:LEU625 3.2 55.6 1.0 O A:MET624 3.4 43.3 1.0 C A:MET624 3.5 53.0 1.0 CG A:LYS623 3.6 42.7 1.0 C32 A:9KI1001 3.6 45.9 1.0 C27 A:9KI1001 3.7 42.7 1.0 CE A:LYS623 3.7 51.0 1.0 CG A:LEU625 3.7 52.9 1.0 CD1 A:LEU637 3.8 43.9 1.0 N A:LEU625 3.9 45.1 1.0 N A:MET624 4.0 38.8 1.0 C26 A:9KI1001 4.1 48.3 1.0 CA A:LEU625 4.2 48.2 1.0 CA A:MET624 4.2 44.7 1.0 CD2 A:LEU637 4.3 43.1 1.0 CD A:LYS623 4.3 40.1 1.0 CG A:LEU637 4.5 41.8 1.0 CB A:LEU625 4.5 53.1 1.0 C A:LYS623 4.6 42.4 1.0 CB A:LEU637 4.8 42.5 1.0 CB A:PHE600 4.8 65.9 1.0 CB A:LYS623 4.9 37.0 1.0 CD1 A:LEU625 5.0 57.5 1.0

Fluorine binding site 2 out of 2 in the C-Kit Kinase Domain in Complex with Avapritinib Derivative 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:43.4 occ:1.00 F30 C:9KI1001 0.0 43.4 1.0 C29 C:9KI1001 1.4 42.5 1.0 C31 C:9KI1001 2.4 40.9 1.0 C28 C:9KI1001 2.4 43.3 1.0 CD2 C:LEU625 3.2 45.0 1.0 O C:MET624 3.5 37.7 1.0 CG C:LEU625 3.5 42.8 1.0 C C:MET624 3.6 37.7 1.0 C32 C:9KI1001 3.6 44.4 1.0 C27 C:9KI1001 3.7 42.5 1.0 CG C:LYS623 3.8 38.6 1.0 CE C:LYS623 3.8 45.1 1.0 CD1 C:LEU637 3.8 36.6 1.0 N C:LEU625 3.8 40.4 1.0 CD2 C:LEU637 4.0 37.5 1.0 CA C:LEU625 4.1 41.5 1.0 C26 C:9KI1001 4.1 46.6 1.0 N C:MET624 4.2 33.7 1.0 CA C:MET624 4.3 38.1 1.0 CB C:LEU625 4.3 43.3 1.0 CG C:LEU637 4.4 36.9 1.0 CD C:LYS623 4.4 42.2 1.0 CD1 C:LEU625 4.6 43.7 1.0 CB C:LEU637 4.7 40.9 1.0 C C:LYS623 4.8 36.0 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