Chlorine 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:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine was determined in the Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062, PDB code: 5y25:

Chlorine binding site 1 out of 1 in 5y25

Go back to Chlorine Binding Sites List in 5y25
Chlorine binding site 1 out of 1 in the Egfr Kinase Domain Mutant (T790M/L858R) with Covalent Ligand Ns-062


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1100

b:71.5
occ:1.00
 CL1 A:8LU1100 0.0 71.5 1.0
C4 A:8LU1100 1.8 69.1 1.0
C1 A:8LU1100 2.7 73.2 1.0
F1 A:8LU1100 2.9 75.2 1.0
C5 A:8LU1100 2.9 66.3 1.0
O A:LEU788 3.2 73.0 1.0
CG A:MET790 3.4 66.2 1.0
O A:ALA743 3.5 67.8 1.0
CB A:LYS745 3.6 75.0 1.0
N A:LYS745 3.6 75.6 1.0
C A:LEU788 3.8 71.1 1.0
CB A:MET790 3.8 65.1 1.0
N A:MET790 3.9 66.5 1.0
C A:ALA743 3.9 68.2 1.0
CB A:LEU788 4.0 70.6 1.0
C6 A:8LU1100 4.1 69.5 1.0
C A:ILE744 4.1 76.3 1.0
C2 A:8LU1100 4.1 74.0 1.0
N A:ILE744 4.1 71.3 1.0
CA A:ILE744 4.2 72.5 1.0
CA A:LYS745 4.2 77.9 1.0
SD A:MET790 4.3 79.3 1.0
CE A:MET790 4.4 64.8 1.0
N A:ILE789 4.4 66.9 1.0
CA A:MET790 4.5 65.5 1.0
CB A:ALA743 4.5 61.7 1.0
CA A:LEU788 4.5 73.2 1.0
C A:ILE789 4.5 66.2 1.0
CA A:ILE789 4.6 67.1 1.0
C3 A:8LU1100 4.7 70.0 1.0
CG A:LYS745 4.8 78.3 1.0
CA A:ALA743 4.8 61.6 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: Sat Dec 12 12:40:03 2020

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