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

Protein crystallography data

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

Other elements in 8wd4:

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

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

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 8wd4

Go back to Fluorine Binding Sites List in 8wd4
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 8wd4

Go back to Fluorine Binding Sites List in 8wd4
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

Reference:

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
Page generated: Wed Jul 16 10:00:30 2025

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