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Fluorine in PDB 6fyz: Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor

Enzymatic activity of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor

All present enzymatic activity of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor:
3.5.1.98;

Protein crystallography data

The structure of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor, PDB code: 6fyz was solved by C.A.Luckhurst, M.C.Maillard, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.70 / 2.15
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 105.530, 105.530, 88.860, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 22.8

Other elements in 6fyz:

The structure of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Sodium (Na) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor (pdb code 6fyz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor, PDB code: 6fyz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6fyz

Go back to Fluorine Binding Sites List in 6fyz
Fluorine binding site 1 out of 3 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:27.6
occ:1.00
 F25 A:EBE2001 0.0 27.6 1.0
C15 A:EBE2001 1.4 27.2 1.0
C16 A:EBE2001 2.4 26.4 1.0
C14 A:EBE2001 2.4 26.2 1.0
C13 A:EBE2001 2.8 26.1 1.0
C20 A:EBE2001 2.9 26.0 1.0
O21 A:EBE2001 3.2 25.0 1.0
CA A:GLY974 3.3 23.6 1.0
CG A:PRO800 3.3 19.0 1.0
N22 A:EBE2001 3.6 26.0 1.0
C17 A:EBE2001 3.6 26.5 1.0
C19 A:EBE2001 3.7 26.2 1.0
CB A:PRO800 3.7 19.5 1.0
N A:GLY974 3.8 22.5 1.0
O A:GLU973 3.9 22.5 1.0
C A:GLU973 4.0 22.4 1.0
C18 A:EBE2001 4.1 26.4 1.0
C3 A:EBE2001 4.3 27.0 1.0
CD A:PRO800 4.4 19.1 1.0
O23 A:EBE2001 4.4 26.0 1.0
O A:GLY811 4.4 23.3 1.0
O A:HOH2153 4.5 27.7 1.0
C A:GLY974 4.6 24.9 1.0
CG A:GLU677 4.6 28.4 1.0
NH1 A:ARG681 4.8 22.8 1.0
CD2 A:PHE812 4.9 25.8 1.0
N A:GLY975 4.9 26.8 1.0
ZN A:ZN2002 5.0 21.1 1.0

Fluorine binding site 2 out of 3 in 6fyz

Go back to Fluorine Binding Sites List in 6fyz
Fluorine binding site 2 out of 3 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2001

b:19.5
occ:1.00
 F25 B:EBE2001 0.0 19.5 1.0
C15 B:EBE2001 1.3 19.9 1.0
C16 B:EBE2001 2.4 19.8 1.0
C14 B:EBE2001 2.4 19.6 1.0
C13 B:EBE2001 2.8 20.4 1.0
C20 B:EBE2001 2.9 19.7 1.0
O21 B:EBE2001 3.2 18.7 1.0
CA B:GLY974 3.3 18.4 1.0
CG B:PRO800 3.4 17.8 1.0
N22 B:EBE2001 3.6 20.0 1.0
C19 B:EBE2001 3.6 20.2 1.0
C17 B:EBE2001 3.6 20.4 1.0
N B:GLY974 3.9 17.9 1.0
CB B:PRO800 3.9 17.6 1.0
O B:GLU973 4.0 18.0 1.0
C18 B:EBE2001 4.1 19.8 1.0
C B:GLU973 4.2 18.2 1.0
C3 B:EBE2001 4.2 21.4 1.0
CG B:GLU677 4.4 21.7 1.0
CD B:PRO800 4.4 17.6 1.0
O B:GLY811 4.4 15.4 1.0
O23 B:EBE2001 4.5 21.0 1.0
C B:GLY974 4.6 18.7 1.0
CD2 B:PHE812 4.7 18.9 1.0
O B:HOH2177 4.7 29.2 1.0
NH2 B:ARG681 4.8 18.3 1.0
N B:GLY975 4.9 19.7 1.0
C2 B:EBE2001 5.0 21.8 1.0
CB B:PHE812 5.0 18.2 1.0

Fluorine binding site 3 out of 3 in 6fyz

Go back to Fluorine Binding Sites List in 6fyz
Fluorine binding site 3 out of 3 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:24.3
occ:1.00
 F25 C:EBE2001 0.0 24.3 1.0
C15 C:EBE2001 1.3 23.5 1.0
C16 C:EBE2001 2.4 23.2 1.0
C14 C:EBE2001 2.4 22.9 1.0
C13 C:EBE2001 2.7 23.4 1.0
C20 C:EBE2001 2.9 22.9 1.0
O21 C:EBE2001 3.2 22.7 1.0
CA C:GLY974 3.3 20.3 1.0
CG C:PRO800 3.4 19.1 1.0
N22 C:EBE2001 3.6 22.5 1.0
C17 C:EBE2001 3.6 23.2 1.0
C19 C:EBE2001 3.6 22.8 1.0
N C:GLY974 3.8 20.0 1.0
CB C:PRO800 3.8 19.2 1.0
O C:GLU973 4.0 20.1 1.0
C C:GLU973 4.1 20.6 1.0
C18 C:EBE2001 4.1 22.9 1.0
C3 C:EBE2001 4.2 23.9 1.0
O C:GLY811 4.4 24.9 1.0
O C:HOH2131 4.4 31.4 1.0
CD C:PRO800 4.4 19.2 1.0
O23 C:EBE2001 4.5 20.3 1.0
CG C:GLU677 4.5 24.9 1.0
C C:GLY974 4.6 21.1 1.0
NH2 C:ARG681 4.8 18.0 1.0
CD2 C:PHE812 4.8 27.4 1.0
C2 C:EBE2001 5.0 24.1 1.0
N C:GLY975 5.0 21.4 1.0

Reference:

C.A.Luckhurst, O.Aziz, V.Beaumont, R.W.Burli, P.Breccia, M.C.Maillard, A.F.Haughan, M.Lamers, P.Leonard, K.L.Matthews, G.Raphy, A.J.Stott, I.Munoz-Sanjuan, B.Thomas, M.Wall, G.Wishart, D.Yates, C.Dominguez. Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor. Bioorg. Med. Chem. Lett. V. 29 83 2019.
ISSN: ESSN 1464-3405
PubMed: 30463802
DOI: 10.1016/J.BMCL.2018.11.009
Page generated: Thu Aug 1 20:17:00 2024

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