Fluorine 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:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	3 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the SMYD2 in Complex with Sgc Probe Bay-598, PDB code: 5arg:
Jump to Fluorine binding site number: 1; 2;

Fluorine 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 Fluorine with other atoms in the F 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:F1432 b:23.7 occ:1.00 F25 A:H411432 0.0 23.7 1.0 C23 A:H411432 1.4 27.7 1.0 F24 A:H411432 2.1 28.1 1.0 O22 A:H411432 2.2 26.5 1.0 C20 A:H411432 3.0 37.6 1.0 C19 A:H411432 3.2 33.8 1.0 CG1 A:VAL179 3.2 33.2 1.0 CA A:THR105 3.4 26.0 1.0 CD2 A:LEU108 3.5 21.9 1.0 OG1 A:THR105 3.5 28.5 1.0 CG2 A:THR105 3.6 29.4 1.0 CB A:THR105 3.7 29.0 1.0 CB A:LEU108 4.1 21.9 1.0 N A:THR105 4.2 25.9 1.0 O A:THR105 4.2 25.0 1.0 C21 A:H411432 4.3 23.2 1.0 C A:THR105 4.3 27.1 1.0 CG A:LEU108 4.3 20.9 1.0 C18 A:H411432 4.5 34.3 1.0 O A:GLU104 4.5 23.9 1.0 O A:HOH2080 4.5 29.0 1.0 CB A:VAL179 4.7 33.8 1.0 C A:GLU104 4.7 26.1 1.0 O A:HOH2045 4.8 35.0 1.0 CB A:SER196 4.9 21.8 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F1432 b:28.1 occ:1.00 F24 A:H411432 0.0 28.1 1.0 C23 A:H411432 1.3 27.7 1.0 F25 A:H411432 2.1 23.7 1.0 O22 A:H411432 2.3 26.5 1.0 CB A:SER196 3.1 21.8 1.0 O A:HOH2080 3.3 29.0 1.0 OG A:SER196 3.3 19.8 1.0 O A:GLU104 3.4 23.9 1.0 C20 A:H411432 3.5 37.6 1.0 CD2 A:LEU108 3.5 21.9 1.0 CA A:THR105 3.5 26.0 1.0 C A:GLU104 3.6 26.1 1.0 N A:THR105 3.6 25.9 1.0 CB A:LEU108 3.7 21.9 1.0 CG A:GLU104 4.0 25.1 1.0 OG1 A:THR105 4.0 28.5 1.0 C19 A:H411432 4.2 33.8 1.0 CG A:LEU108 4.3 20.9 1.0 CB A:GLU104 4.3 27.6 1.0 CB A:THR105 4.3 29.0 1.0 C21 A:H411432 4.5 23.2 1.0 CA A:SER196 4.6 19.6 1.0 CA A:GLU104 4.6 28.4 1.0 C A:THR105 4.7 27.1 1.0 O A:THR105 4.9 25.0 1.0 OE2 A:GLU104 4.9 26.6 1.0 CG2 A:THR105 4.9 29.4 1.0 O A:HOH2021 5.0 43.0 1.0 CD A:GLU104 5.0 26.0 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