Fluorine in PDB 7o2r: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985, PDB code: 7o2r was solved by K.Zrubek, G.Sandrone, C.D.Cukier, A.Stevenazzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.63 / 2.30
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.966, 84.212, 94.977, 90, 90, 90
R / Rfree (%)	19.9 / 26

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Iodine	(I)	6 atoms
Potassium	(K)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 (pdb code 7o2r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985, PDB code: 7o2r:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:47.5 occ:1.00 F1 A:V05801 0.0 47.5 1.0 C4 A:V05801 1.4 43.5 1.0 C3 A:V05801 2.3 44.3 1.0 C5 A:V05801 2.3 46.1 1.0 C6 A:V05801 2.8 48.5 1.0 CA A:GLY582 3.1 31.9 1.0 CB A:SER531 3.1 26.8 1.0 CZ A:PHE643 3.2 35.0 1.0 N2 A:V05801 3.3 53.0 1.0 N3 A:V05801 3.3 62.7 1.0 CE1 A:PHE583 3.4 35.0 1.0 CE1 A:PHE643 3.5 34.7 1.0 C12 A:V05801 3.6 47.3 1.0 CE2 A:PHE643 3.6 34.8 1.0 C2 A:V05801 3.6 49.0 1.0 OG A:SER531 3.6 27.0 1.0 C A:GLY582 3.8 27.4 1.0 CZ A:PHE583 3.8 34.3 1.0 CD1 A:PHE583 3.8 31.3 1.0 O A:SER531 3.9 24.5 1.0 C13 A:V05801 4.1 50.5 1.0 N A:GLY582 4.1 32.5 1.0 O A:GLY582 4.2 23.2 1.0 CD1 A:PHE643 4.2 38.9 1.0 CD2 A:PHE643 4.3 35.3 1.0 N7 A:V05801 4.4 52.1 1.0 CG A:PHE583 4.4 31.7 1.0 N A:PHE583 4.4 28.9 1.0 CE2 A:PHE583 4.4 34.4 1.0 N4 A:V05801 4.4 58.3 1.0 CA A:SER531 4.4 27.7 1.0 CG A:PHE643 4.5 36.4 1.0 C A:SER531 4.7 28.6 1.0 CD2 A:PHE583 4.7 32.4 1.0 F2 A:V05801 4.7 47.3 1.0 C1 A:V05801 4.9 48.9 1.0 C7 A:V05801 4.9 58.3 1.0 O A:ASN530 4.9 29.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3985 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:47.3 occ:1.00 F2 A:V05801 0.0 47.3 1.0 C12 A:V05801 1.3 47.3 1.0 C13 A:V05801 2.3 50.5 1.0 C5 A:V05801 2.4 46.1 1.0 C6 A:V05801 2.8 48.5 1.0 N7 A:V05801 3.5 52.1 1.0 NE2 A:HIS614 3.5 25.1 1.0 N2 A:V05801 3.6 53.0 1.0 C4 A:V05801 3.6 43.5 1.0 C2 A:V05801 3.6 49.0 1.0 CE1 A:HIS614 4.0 23.9 1.0 CD1 A:LEU712 4.0 50.4 1.0 C3 A:V05801 4.1 44.3 1.0 CD2 A:HIS614 4.4 25.5 1.0 CB A:PHE643 4.4 34.8 1.0 CG A:PHE643 4.5 36.4 1.0 CB A:LEU712 4.5 43.4 1.0 CG A:LEU712 4.6 47.8 1.0 CD2 A:PHE643 4.7 35.3 1.0 CD2 A:LEU712 4.7 55.4 1.0 F1 A:V05801 4.7 47.5 1.0 C1 A:V05801 4.8 48.9 1.0 C7 A:V05801 4.8 58.3 1.0 N1 A:V05801 4.9 46.9 1.0 N3 A:V05801 4.9 62.7 1.0 ND1 A:HIS614 4.9 24.8 1.0 CZ A:PHE583 5.0 34.3 1.0

G.Sandrone, C.D.Cukier, K.Zrubek, M.Marchini, B.Vergani, G.Caprini, G.Fossati, C.Steinkuhler, A.Stevenazzi. Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00425