Chlorine in PDB 4ynd: The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

All present enzymatic activity of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2:
2.1.1.43;

The structure of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2, PDB code: 4ynd was solved by R.F.Sweis, Z.Wang, M.Algire, C.H.Arrowsmith, P.J.Brown, G.C.Chiang, J.Guo, C.G.Jakob, S.Kennedy, F.Li, N.B.Soni, M.Vedadi, W.N.Pappano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.67 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.796, 71.301, 118.930, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.3

The structure of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Chlorine atom in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 (pdb code 4ynd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2, PDB code: 4ynd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:46.5 occ:1.00 CL1 A:4GQ504 0.0 46.5 1.0 C11 A:4GQ504 1.7 45.8 1.0 C5 A:4GQ504 2.7 45.4 1.0 C12 A:4GQ504 2.7 45.5 1.0 CL2 A:4GQ504 3.1 46.7 1.0 CD2 A:LEU141 3.6 39.3 1.0 CD1 A:ILE149 3.6 42.4 1.0 CB A:ASN180 3.9 23.4 1.0 C3 A:4GQ504 4.0 45.1 1.0 C6 A:4GQ504 4.0 44.6 1.0 CA A:ALA177 4.0 25.4 1.0 CG A:ASN180 4.1 39.9 1.0 CD A:LYS145 4.2 55.2 1.0 ND2 A:ASN180 4.2 30.4 1.0 CG A:LYS145 4.2 47.3 1.0 CB A:ALA177 4.3 26.2 1.0 CG1 A:ILE149 4.4 35.8 1.0 CB A:LYS145 4.4 36.6 1.0 C7 A:4GQ504 4.5 44.4 1.0 O A:ALA177 4.6 28.4 1.0 CE A:LYS145 4.8 63.3 1.0 OD1 A:ASN180 4.8 32.4 1.0 C A:ALA177 4.8 28.7 1.0 N A:ALA177 4.9 25.8 1.0 CG A:LEU141 4.9 37.0 1.0 O A:PHE176 5.0 29.3 1.0

Chlorine binding site 2 out of 2 in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:46.7 occ:1.00 CL2 A:4GQ504 0.0 46.7 1.0 C12 A:4GQ504 1.7 45.5 1.0 C6 A:4GQ504 2.7 44.6 1.0 C11 A:4GQ504 2.7 45.8 1.0 CL1 A:4GQ504 3.1 46.5 1.0 CG A:LYS145 3.8 47.3 1.0 O A:LYS145 3.9 37.7 1.0 CG1 A:ILE149 3.9 35.8 1.0 C7 A:4GQ504 4.0 44.4 1.0 C5 A:4GQ504 4.0 45.4 1.0 CB A:LYS145 4.0 36.6 1.0 OD1 A:ASN180 4.1 32.4 1.0 ND2 A:ASN180 4.1 30.4 1.0 CG A:ASN180 4.1 39.9 1.0 CA A:LYS145 4.1 34.3 1.0 CD1 A:ILE149 4.2 42.4 1.0 CB A:LEU148 4.2 32.9 1.0 CD1 A:LEU148 4.4 37.4 1.0 C A:LYS145 4.5 38.1 1.0 C3 A:4GQ504 4.5 45.1 1.0 CD A:LYS145 4.7 55.2 1.0 N A:ILE149 4.9 32.5 1.0 CB A:ASN180 4.9 23.4 1.0 CG A:LEU148 5.0 37.4 1.0

R.F.Sweis, Z.Wang, M.Algire, C.H.Arrowsmith, P.J.Brown, G.C.Chiang, J.Guo, C.G.Jakob, S.Kennedy, F.Li, N.B.Soni, M.Vedadi, W.N.Pappano. The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 Acs Med.Chem.Lett. 2015.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACSMEDCHEMLETT.5B00124