Fluorine in PDB 5y25: Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062

All present enzymatic activity of Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062:
2.7.10.1;

The structure of Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062, PDB code: 5y25 was solved by M.Shiroishi, Y.Abe, J.M.M.Caaveiro, S.Sakamoto, S.Morimoto, H.Fuchida, N.Shindo, A.Ojida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 3.10
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	148.291, 148.291, 148.291, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.6

The structure of Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062 (pdb code 5y25). 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 Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062, PDB code: 5y25:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1100 b:75.2 occ:1.00 F1 A:8LU1100 0.0 75.2 1.0 C1 A:8LU1100 1.4 73.2 1.0 C4 A:8LU1100 2.3 69.1 1.0 C2 A:8LU1100 2.5 74.0 1.0 CL1 A:8LU1100 2.9 71.5 1.0 CE A:LYS745 3.4 79.1 1.0 CD1 A:LEU788 3.6 79.3 1.0 SD A:MET790 3.7 79.3 1.0 C3 A:8LU1100 3.7 70.0 1.0 CB A:LEU788 3.7 70.6 1.0 C5 A:8LU1100 3.8 66.3 1.0 OE2 A:GLU762 3.9 86.0 1.0 CG A:MET790 3.9 66.2 1.0 CB A:LYS745 3.9 75.0 1.0 NZ A:LYS745 4.2 83.8 1.0 C6 A:8LU1100 4.2 69.5 1.0 CD A:LYS745 4.3 79.4 1.0 CE A:MET790 4.3 64.8 1.0 CG A:LEU788 4.3 73.2 1.0 CG A:LYS745 4.5 78.3 1.0 CD A:GLU762 4.9 87.5 1.0

Fluorine binding site 2 out of 2 in the Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1100 b:70.2 occ:1.00 F2 A:8LU1100 0.0 70.2 1.0 C19 A:8LU1100 1.4 69.3 1.0 C18 A:8LU1100 2.4 65.4 1.0 O1 A:8LU1100 2.7 64.9 1.0 SG A:CYS797 2.8 71.0 1.0 CB A:CYS797 3.0 59.0 1.0 CB A:ARG841 3.4 59.5 1.0 N5 A:8LU1100 3.7 64.4 1.0 CA A:ARG841 3.7 61.8 1.0 O A:ARG841 3.8 65.0 1.0 C A:ARG841 4.2 61.9 1.0 C17 A:8LU1100 4.3 67.6 1.0 OD2 A:ASP800 4.4 69.8 1.0 CA A:CYS797 4.5 57.4 1.0 CG A:ARG841 4.7 61.7 1.0 C14 A:8LU1100 4.9 69.0 1.0

N.Shindo, H.Fuchida, M.Sato, K.Watari, T.Shibata, K.Kuwata, C.Miura, K.Okamoto, Y.Hatsuyama, K.Tokunaga, S.Sakamoto, S.Morimoto, Y.Abe, M.Shiroishi, J.M.M.Caaveiro, T.Ueda, T.Tamura, N.Matsunaga, T.Nakao, S.Koyanagi, S.Ohdo, Y.Yamaguchi, I.Hamachi, M.Ono, A.Ojida. Selective and Reversible Modification of Kinase Cysteines with Chlorofluoroacetamides. Nat.Chem.Biol. V. 15 250 2019.
ISSN: ESSN 1552-4469
PubMed: 30643284
DOI: 10.1038/S41589-018-0204-3