Fluorine in PDB 5arf: SMYD2 in Complex with Small Molecule Inhibitor Compound-2

All present enzymatic activity of SMYD2 in Complex with Small Molecule Inhibitor Compound-2:
2.1.1.43;

The structure of SMYD2 in Complex with Small Molecule Inhibitor Compound-2, PDB code: 5arf 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)	47.59 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.493, 51.759, 69.568, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 30.1

The structure of SMYD2 in Complex with Small Molecule Inhibitor Compound-2 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	3 atoms

The binding sites of Fluorine atom in the SMYD2 in Complex with Small Molecule Inhibitor Compound-2 (pdb code 5arf). 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 Small Molecule Inhibitor Compound-2, PDB code: 5arf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the SMYD2 in Complex with Small Molecule Inhibitor Compound-2


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 Small Molecule Inhibitor Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:17.5 occ:1.00 FBH A:I9H1001 0.0 17.5 1.0 CBF A:I9H1001 1.4 15.5 1.0 FBG A:I9H1001 2.2 17.9 1.0 OBE A:I9H1001 2.3 15.7 1.0 CB A:SER196 3.0 20.1 1.0 OG A:SER196 3.3 20.9 1.0 O A:GLU104 3.4 25.9 1.0 CBB A:I9H1001 3.5 19.8 1.0 C A:GLU104 3.6 27.2 1.0 CD2 A:LEU108 3.6 21.6 1.0 CB A:LEU108 3.6 22.8 1.0 N A:THR105 3.7 28.5 1.0 CA A:THR105 3.7 28.5 1.0 O A:HOH2065 3.7 16.6 1.0 CG A:GLU104 3.9 24.5 1.0 OG1 A:THR105 4.1 29.9 1.0 CBD A:I9H1001 4.2 17.6 1.0 CG A:LEU108 4.2 21.8 1.0 CB A:GLU104 4.2 26.8 1.0 CB A:THR105 4.5 30.5 1.0 CA A:SER196 4.5 18.9 1.0 CA A:GLU104 4.5 28.2 1.0 CAY A:I9H1001 4.5 10.2 1.0 C A:THR105 4.7 29.1 1.0 OE2 A:GLU104 4.7 22.3 1.0 O A:THR105 4.8 28.1 1.0 CD A:GLU104 4.9 23.9 1.0 CA A:LEU108 4.9 23.6 1.0 C A:SER196 5.0 18.8 1.0 N A:LEU108 5.0 24.9 1.0

Fluorine binding site 2 out of 2 in the SMYD2 in Complex with Small Molecule Inhibitor Compound-2


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 Small Molecule Inhibitor Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:17.9 occ:1.00 FBG A:I9H1001 0.0 17.9 1.0 CBF A:I9H1001 1.3 15.5 1.0 OBE A:I9H1001 2.1 15.7 1.0 FBH A:I9H1001 2.2 17.5 1.0 CBB A:I9H1001 2.9 19.8 1.0 CBD A:I9H1001 3.0 17.6 1.0 CG1 A:VAL179 3.2 27.3 1.0 OG1 A:THR105 3.3 29.9 1.0 CA A:THR105 3.3 28.5 1.0 CB A:THR105 3.6 30.5 1.0 CD2 A:LEU108 3.7 21.6 1.0 CG2 A:THR105 3.7 31.1 1.0 CB A:LEU108 4.0 22.8 1.0 N A:THR105 4.1 28.5 1.0 O A:THR105 4.1 28.1 1.0 C A:THR105 4.2 29.1 1.0 CAY A:I9H1001 4.3 10.2 1.0 CBC A:I9H1001 4.4 17.5 1.0 CG A:LEU108 4.4 21.8 1.0 O A:GLU104 4.4 25.9 1.0 C A:GLU104 4.5 27.2 1.0 O A:HOH2036 4.7 19.8 1.0 CB A:VAL179 4.8 29.1 1.0 O A:HOH2065 4.8 16.6 1.0 CB A:SER196 4.9 20.1 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