Fluorine in PDB 8wd4: Egfr(L858R/T790/C797S) in Complex with Compound 5J

The structure of Egfr(L858R/T790/C797S) in Complex with Compound 5J, PDB code: 8wd4 was solved by Y.Nishikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.96 / 2.55
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	145.327, 145.327, 145.327, 90, 90, 90
R / Rfree (%)	19.9 / 23

The structure of Egfr(L858R/T790/C797S) in Complex with Compound 5J also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Egfr(L858R/T790/C797S) in Complex with Compound 5J (pdb code 8wd4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Egfr(L858R/T790/C797S) in Complex with Compound 5J, PDB code: 8wd4:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Egfr(L858R/T790/C797S) in Complex with Compound 5J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Egfr(L858R/T790/C797S) in Complex with Compound 5J within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:86.4 occ:1.00 F36 A:W7W1101 0.0 86.4 1.0 C35 A:W7W1101 1.4 78.9 1.0 F37 A:W7W1101 2.3 95.7 1.0 C34 A:W7W1101 2.4 77.4 1.0 N32 A:W7W1101 2.6 70.9 1.0 C33 A:W7W1101 3.0 76.5 1.0 CD2 A:LEU718 3.1 81.5 1.0 C30 A:W7W1101 3.2 72.3 1.0 CD1 A:LEU792 3.6 55.5 1.0 C28 A:W7W1101 3.7 62.4 1.0 O31 A:W7W1101 3.9 73.9 1.0 C27 A:W7W1101 3.9 69.6 1.0 CD1 A:LEU718 3.9 70.8 1.0 O A:PRO794 4.0 66.2 1.0 CG A:LEU718 4.1 71.3 1.0 CG A:LEU792 4.2 50.9 1.0 CA A:PRO794 4.3 55.6 1.0 CD2 A:LEU792 4.5 55.4 1.0 C A:PRO794 4.5 59.2 1.0 O A:MET793 4.5 54.9 1.0 N29 A:W7W1101 4.8 56.9 1.0 CD A:LYS728 4.8 78.1 1.0 C A:MET793 4.9 52.7 1.0 N A:PRO794 4.9 57.1 1.0 CG A:LYS728 5.0 68.0 1.0

Fluorine binding site 2 out of 2 in the Egfr(L858R/T790/C797S) in Complex with Compound 5J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Egfr(L858R/T790/C797S) in Complex with Compound 5J within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:95.7 occ:1.00 F37 A:W7W1101 0.0 95.7 1.0 C35 A:W7W1101 1.4 78.9 1.0 F36 A:W7W1101 2.3 86.4 1.0 C34 A:W7W1101 2.4 77.4 1.0 CD2 A:LEU718 3.8 81.5 1.0 C33 A:W7W1101 3.8 76.5 1.0 CD A:LYS728 4.1 78.1 1.0 N32 A:W7W1101 4.3 70.9 1.0 NZ A:LYS728 4.3 88.5 1.0 O A:PRO794 4.4 66.2 1.0 CE A:LYS728 4.5 88.9 1.0 CE A:LYS716 4.6 79.6 1.0 NZ A:LYS716 4.7 78.8 0.0 CG A:LYS728 5.0 68.0 1.0

H.Kageji, T.Momose, Y.Nagamoto, N.Togashi, I.Yasumatsu, Y.Nishikawa, K.Kihara, K.Hiramoto, M.Minami, N.Kasanuki, T.Isoyama, H.Naito. Synthesis, Activity, and Their Relationships of 2,4-Diaminonicotinamide Derivatives As Egfr Inhibitors Targeting C797S Mutation. Bioorg.Med.Chem.Lett. 29575 2023.
ISSN: ESSN 1464-3405
PubMed: 38065292
DOI: 10.1016/J.BMCL.2023.129575