Chlorine in PDB 5arg: SMYD2 in Complex with Sgc Probe Bay-598

All present enzymatic activity of SMYD2 in Complex with Sgc Probe Bay-598:
2.1.1.43;

The structure of SMYD2 in Complex with Sgc Probe Bay-598, PDB code: 5arg was solved by R.C.Hillig, V.Badock, N.Barak, T.Stellfeld, E.Eggert, A.Ter Laak, J.Weiske, C.D.Christ, S.Koehr, D.Stoeckigt, J.Mowat, T.Mueller, A.E.Fernandez-Montalvan, I.V.Hartung, C.Stresemann, T.Brumby, H.Weinmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.72 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.343, 69.600, 131.115, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.3

The structure of SMYD2 in Complex with Sgc Probe Bay-598 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Zinc	(Zn)	3 atoms

The binding sites of Chlorine atom in the SMYD2 in Complex with Sgc Probe Bay-598 (pdb code 5arg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the SMYD2 in Complex with Sgc Probe Bay-598, PDB code: 5arg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the SMYD2 in Complex with Sgc Probe Bay-598


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of SMYD2 in Complex with Sgc Probe Bay-598 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1432 b:28.2 occ:1.00 CL10 A:H411432 0.0 28.2 1.0 C5 A:H411432 1.7 24.8 1.0 C6 A:H411432 2.7 15.6 1.0 C4 A:H411432 2.7 22.3 1.0 CL7 A:H411432 3.1 28.2 1.0 CE A:SAM1434 3.4 37.8 1.0 O A:ASN182 3.5 29.3 1.0 CZ A:PHE184 3.7 30.1 1.0 CB A:ALA203 3.7 31.4 1.0 CE1 A:PHE184 3.7 29.3 1.0 CA A:ASN182 3.8 31.7 1.0 C A:ASN182 3.8 30.5 1.0 CA A:ALA203 3.8 34.3 1.0 C8 A:H411432 4.0 24.4 1.0 C3 A:H411432 4.0 19.4 1.0 O A:CYS181 4.2 33.4 1.0 O A:HOH2061 4.3 27.4 1.0 CE2 A:PHE184 4.3 25.8 1.0 C9 A:H411432 4.4 19.1 1.0 O A:GLY183 4.5 25.5 1.0 CD1 A:PHE184 4.5 24.4 1.0 O A:ALA203 4.5 37.9 1.0 CB A:ASN182 4.6 31.4 1.0 C A:ALA203 4.7 36.9 1.0 N A:GLY183 4.7 28.2 1.0 N A:ASN182 4.8 32.8 1.0 N A:ALA203 4.8 35.6 1.0 OD1 A:ASN182 4.9 35.6 1.0 CE1 A:TYR240 4.9 35.6 1.0 C A:CYS181 4.9 37.1 1.0 CD2 A:PHE184 4.9 22.4 1.0 CZ A:TYR240 5.0 40.2 1.0

Chlorine binding site 2 out of 2 in the SMYD2 in Complex with Sgc Probe Bay-598


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of SMYD2 in Complex with Sgc Probe Bay-598 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1432 b:28.2 occ:1.00 CL7 A:H411432 0.0 28.2 1.0 C6 A:H411432 1.6 15.6 1.0 C8 A:H411432 2.6 24.4 1.0 C5 A:H411432 2.7 24.8 1.0 CL10 A:H411432 3.1 28.2 1.0 O A:VAL202 3.5 42.5 1.0 CZ A:PHE184 3.6 30.1 1.0 CE1 A:TYR240 3.6 35.6 1.0 CG2 A:THR238 3.7 36.7 1.0 O A:MET205 3.7 42.1 1.0 C9 A:H411432 3.9 19.1 1.0 CE2 A:PHE184 3.9 25.8 1.0 C4 A:H411432 3.9 22.3 1.0 CA A:ALA203 4.0 34.3 1.0 C A:VAL202 4.2 36.1 1.0 CD1 A:TYR240 4.2 34.8 1.0 CZ A:TYR240 4.4 40.2 1.0 C3 A:H411432 4.4 19.4 1.0 N A:ALA203 4.5 35.6 1.0 CG1 A:VAL202 4.5 32.0 1.0 OH A:TYR240 4.5 44.2 1.0 CB A:MET205 4.6 43.1 1.0 C A:ALA203 4.6 36.9 1.0 CE1 A:PHE184 4.6 29.3 1.0 C A:MET205 4.7 44.8 1.0 O A:ALA203 4.7 37.9 1.0 N A:MET205 4.7 42.8 1.0 CE A:SAM1434 4.8 37.8 1.0 CA A:MET205 4.9 44.5 1.0 CB A:ALA203 4.9 31.4 1.0

E.Eggert, R.C.Hillig, S.Kohr, D.Stockigt, J.Weiske, N.Barak, J.Mowat, T.Brumby, C.D.Christ, A.Ter Laak, T.Lang, A.E.Fernandez-Montalvan, V.Badock, H.Weinmann, I.V.Hartung, D.Barsyte-Lovejoy, M.Szewczyk, S.Kennedy, F.Li, M.Vedadi, P.J.Brown, V.Santhakumar, C.H.Arrowsmith, T.Stellfeld, C.Stresemann. Discovery and Characterization of A Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) For the Protein Lysine Methyltransferase SMYD2. J.Med.Chem. V. 59 4578 2016.
ISSN: ISSN 0022-2623
PubMed: 27075367
DOI: 10.1021/ACS.JMEDCHEM.5B01890