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Sodium 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:

Fluorine (F) 3 atoms
Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor, PDB code: 6fyz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6fyz

Go back to Sodium Binding Sites List in 6fyz
Sodium 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 Sodium with other atoms in the Na 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:Na2004

b:19.1
occ:1.00
 O A:ASP854 2.3 19.6 1.0
O A:HOH2154 2.3 16.1 1.0
O A:VAL857 2.4 21.7 1.0
O A:HOH2149 2.4 22.2 1.0
O A:PHE851 2.5 16.9 1.0
C A:ASP854 3.5 20.8 1.0
O A:PHE888 3.5 19.4 1.0
C A:PHE851 3.6 17.4 1.0
C A:VAL857 3.6 21.0 1.0
CB A:PHE888 3.8 19.1 1.0
CB A:PHE851 3.9 17.9 1.0
N A:ASP854 4.0 21.2 1.0
C A:PHE888 4.1 19.0 1.0
O A:HOH2111 4.2 27.6 1.0
CA A:ASP854 4.2 20.8 1.0
CB A:ASP854 4.3 20.6 1.0
CA A:PHE851 4.3 17.4 1.0
CA A:VAL857 4.5 20.9 1.0
N A:PRO855 4.5 20.9 1.0
CB A:VAL857 4.5 20.8 1.0
N A:VAL857 4.6 20.6 1.0
N A:LEU858 4.6 20.5 1.0
O A:TYR852 4.6 18.4 1.0
N A:TYR852 4.6 17.3 1.0
CA A:PHE888 4.6 19.1 1.0
C A:TYR852 4.6 18.8 1.0
N A:TYR859 4.6 20.4 1.0
CA A:LEU858 4.6 20.8 1.0
CA A:PRO855 4.7 21.6 1.0
CA A:TYR852 4.7 17.6 1.0
O A:GLY885 4.8 24.4 1.0
N A:ASN889 4.8 18.9 1.0
CG A:PHE888 5.0 19.1 1.0

Sodium binding site 2 out of 3 in 6fyz

Go back to Sodium Binding Sites List in 6fyz
Sodium 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 Sodium with other atoms in the Na 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:Na2004

b:21.3
occ:1.00
 O B:ASP854 2.2 25.2 1.0
O B:VAL857 2.3 22.9 1.0
O B:HOH2137 2.4 23.4 1.0
O B:PHE851 2.5 19.4 1.0
O B:HOH2144 2.5 21.6 1.0
C B:ASP854 3.4 26.1 1.0
O B:PHE888 3.5 21.2 1.0
C B:VAL857 3.5 22.7 1.0
C B:PHE851 3.6 19.9 1.0
CB B:PHE888 3.8 22.6 1.0
N B:ASP854 3.9 26.6 1.0
CB B:PHE851 3.9 20.9 1.0
CA B:ASP854 4.0 26.4 1.0
C B:PHE888 4.1 21.5 1.0
CB B:ASP854 4.2 26.5 1.0
O B:HOH2160 4.2 18.1 1.0
CA B:VAL857 4.3 22.5 1.0
CA B:PHE851 4.3 20.0 1.0
CB B:VAL857 4.4 22.6 1.0
N B:VAL857 4.4 22.6 1.0
N B:PRO855 4.4 26.3 1.0
O B:TYR852 4.5 20.3 1.0
N B:LEU858 4.6 21.2 1.0
C B:TYR852 4.6 21.9 1.0
CA B:PHE888 4.6 22.2 1.0
N B:TYR852 4.6 20.3 1.0
CA B:PRO855 4.7 25.5 1.0
CA B:TYR852 4.7 20.4 1.0
CA B:LEU858 4.7 21.5 1.0
O B:GLY885 4.8 27.2 1.0
CG1 B:VAL857 4.9 22.5 1.0
N B:TYR859 4.9 20.5 1.0
CA B:GLY885 4.9 27.2 1.0
CG B:PHE888 5.0 22.7 1.0
C B:SER853 5.0 26.3 1.0
N B:ASN889 5.0 20.1 1.0

Sodium binding site 3 out of 3 in 6fyz

Go back to Sodium Binding Sites List in 6fyz
Sodium 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 Sodium with other atoms in the Na 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:Na2004

b:34.3
occ:1.00
 O C:HOH2158 2.2 30.8 1.0
O C:VAL857 2.3 32.4 1.0
O C:ASP854 2.4 38.3 1.0
O C:HOH2135 2.4 22.2 1.0
O C:PHE851 2.4 28.4 1.0
C C:ASP854 3.5 37.1 1.0
C C:VAL857 3.5 31.9 1.0
C C:PHE851 3.6 30.5 1.0
O C:PHE888 3.6 30.5 1.0
CB C:PHE888 3.8 31.4 1.0
CB C:PHE851 4.0 29.0 1.0
N C:ASP854 4.0 37.7 1.0
O C:HOH2128 4.1 29.4 1.0
CA C:ASP854 4.1 38.2 1.0
C C:PHE888 4.2 30.4 1.0
CB C:ASP854 4.3 38.9 1.0
CA C:PHE851 4.4 29.5 1.0
CA C:VAL857 4.4 32.0 1.0
CB C:VAL857 4.4 32.4 1.0
O C:TYR852 4.5 33.6 1.0
N C:LEU858 4.5 30.6 1.0
N C:PRO855 4.5 35.5 1.0
N C:VAL857 4.6 31.9 1.0
C C:TYR852 4.6 34.6 1.0
N C:TYR852 4.6 32.1 1.0
CA C:LEU858 4.6 30.3 1.0
CA C:PHE888 4.7 31.4 1.0
CA C:TYR852 4.7 34.2 1.0
N C:TYR859 4.7 28.2 1.0
O C:GLY885 4.8 34.5 1.0
CA C:PRO855 4.8 34.7 1.0
N C:ASN889 5.0 28.6 1.0
C C:SER853 5.0 37.7 1.0
CG C:PHE888 5.0 32.2 1.0
CA C:GLY885 5.0 37.2 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: Tue Oct 8 08:51:10 2024

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