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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5y25:

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

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

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 5y25

Go back to Fluorine Binding Sites List in 5y25
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 5y25

Go back to Fluorine Binding Sites List in 5y25
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

Reference:

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
Page generated: Tue Jul 15 09:20:06 2025

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