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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5arf:

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

Fluorine Binding Sites:

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 5arf

Go back to Fluorine Binding Sites List in 5arf
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 5arf

Go back to Fluorine Binding Sites List in 5arf
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

Reference:

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
Page generated: Thu Aug 1 07:50:28 2024

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