Fluorine in PDB 2vqj: Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor

The structure of Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqj was solved by M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.00 / 2.1
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	106.770, 137.562, 68.993, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.6

The structure of Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor (pdb code 2vqj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqj:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1414 b:32.0 occ:1.00 F1 A:TFG1414 0.0 32.0 1.0 C6 A:TFG1414 1.3 35.9 1.0 F3 A:TFG1414 2.1 34.6 1.0 F2 A:TFG1414 2.2 36.4 1.0 C5 A:TFG1414 2.4 39.1 1.0 O2 A:TFG1414 2.9 39.3 1.0 C2 A:TFG1414 2.9 42.9 1.0 O A:GLY167 2.9 38.4 1.0 C1 A:TFG1414 2.9 41.6 1.0 CD2 A:HIS159 3.1 30.1 1.0 NE2 A:HIS159 3.4 30.2 1.0 O3 A:TFG1414 3.6 38.3 1.0 CG A:PRO156 3.7 34.7 1.0 CB A:PRO156 3.7 34.3 1.0 SG A:CYS169 3.8 33.0 1.0 C A:GLY167 4.0 38.2 1.0 NE2 A:HIS158 4.2 27.4 1.0 C3 A:TFG1414 4.2 44.2 1.0 CD2 A:HIS158 4.3 28.3 1.0 CG A:HIS159 4.4 29.7 1.0 S1 A:TFG1414 4.6 44.8 1.0 CE1 A:HIS159 4.6 30.6 1.0 CD1 A:PHE168 4.6 43.0 1.0 CA A:GLY167 4.7 38.4 1.0 ZN A:ZN1415 4.8 30.7 1.0 CB A:PHE168 4.8 38.3 1.0 CD A:PRO156 4.9 35.0 1.0

Fluorine binding site 2 out of 3 in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1414 b:36.4 occ:1.00 F2 A:TFG1414 0.0 36.4 1.0 C6 A:TFG1414 1.3 35.9 1.0 F3 A:TFG1414 2.1 34.6 1.0 F1 A:TFG1414 2.2 32.0 1.0 C5 A:TFG1414 2.3 39.1 1.0 O3 A:TFG1414 2.7 38.3 1.0 C1 A:TFG1414 3.0 41.6 1.0 CG A:PRO156 3.2 34.7 1.0 C2 A:TFG1414 3.4 42.9 1.0 O2 A:TFG1414 3.5 39.3 1.0 O A:HOH2226 3.8 32.6 1.0 CA A:GLY330 3.9 32.0 1.0 CB A:PRO156 4.0 34.3 1.0 O A:HOH2001 4.0 57.7 1.0 O A:GLY167 4.0 38.4 1.0 CD1 A:PHE168 4.1 43.0 1.0 N A:GLY330 4.3 31.8 1.0 CD A:PRO156 4.4 35.0 1.0 S1 A:TFG1414 4.5 44.8 1.0 CB A:PHE168 4.6 38.3 1.0 C3 A:TFG1414 4.7 44.2 1.0 ZN A:ZN1415 4.8 30.7 1.0 CG A:PHE168 4.8 40.0 1.0 C A:GLU329 4.9 31.1 1.0 O A:GLU329 5.0 30.9 1.0 CE1 A:PHE168 5.0 44.1 1.0

Fluorine binding site 3 out of 3 in the Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of HDAC4 Catalytic Domain Bound to A Trifluoromethylketone Inhbitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1414 b:34.6 occ:1.00 F3 A:TFG1414 0.0 34.6 1.0 C6 A:TFG1414 1.3 35.9 1.0 F2 A:TFG1414 2.1 36.4 1.0 F1 A:TFG1414 2.1 32.0 1.0 C5 A:TFG1414 2.3 39.1 1.0 O2 A:TFG1414 2.6 39.3 1.0 O3 A:TFG1414 2.8 38.3 1.0 N A:GLY330 3.0 31.8 1.0 CA A:GLY330 3.1 32.0 1.0 CG A:PRO156 3.3 34.7 1.0 CB A:PRO156 3.4 34.3 1.0 OD1 A:ASP196 3.5 27.6 1.0 C A:GLU329 3.6 31.1 1.0 C1 A:TFG1414 3.7 41.6 1.0 ZN A:ZN1415 3.8 30.7 1.0 NE2 A:HIS158 3.8 27.4 1.0 O A:GLU329 4.2 30.9 1.0 CD2 A:HIS158 4.2 28.3 1.0 CB A:GLU329 4.3 30.3 1.0 CG A:ASP196 4.3 27.1 1.0 CA A:GLU329 4.4 30.1 1.0 C2 A:TFG1414 4.4 42.9 1.0 OD2 A:ASP196 4.4 29.0 1.0 O A:HOH2226 4.5 32.6 1.0 NE2 A:HIS159 4.5 30.2 1.0 C A:GLY330 4.6 32.7 1.0 CD2 A:HIS159 4.7 30.1 1.0 CD A:PRO156 4.8 35.0 1.0 CA A:PRO156 4.9 34.1 1.0 OE1 A:GLU329 4.9 30.2 1.0 O A:GLY167 4.9 38.4 1.0 CE1 A:HIS158 4.9 27.6 1.0 OD2 A:ASP290 5.0 28.8 1.0

M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi. Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals A Regulatory Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200