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Sodium in PDB 5a2s: Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors

Enzymatic activity of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors

All present enzymatic activity of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors:
3.5.1.98;

Protein crystallography data

The structure of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors, PDB code: 5a2s was solved by C.A.Luckhurst, P.Breccia, A.J.Stott, O.Aziz, H.Birch, R.W.Burli, S.Hughes, R.E.Jarvis, M.Lamers, P.Leonard, K.L.Matthews, G.Mcallister, S.Pollack, E.Saville-Stones, G.Wishart, D.Yates, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 161.63 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.948, 82.141, 161.626, 90.00, 90.00, 90.00
R / Rfree (%) 18.523 / 25.647

Other elements in 5a2s:

The structure of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors (pdb code 5a2s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors, PDB code: 5a2s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5a2s

Go back to Sodium Binding Sites List in 5a2s
Sodium binding site 1 out of 2 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:22.7
occ:1.00
O A:ASP840 2.8 18.0 1.0
OG A:SER861 2.8 20.4 1.0
OD1 A:ASP838 2.9 16.9 1.0
O A:HIS842 3.0 19.1 1.0
O A:ASP838 3.0 17.9 1.0
O A:LEU862 3.1 21.0 1.0
CG A:ASP838 3.2 17.3 1.0
C A:ASP838 3.6 17.8 1.0
C A:LEU862 3.8 20.6 1.0
OD2 A:ASP838 3.8 17.1 1.0
CB A:HIS863 3.8 21.2 1.0
CB A:SER861 3.8 20.5 1.0
CB A:ASP838 3.8 17.6 1.0
C A:ASP840 3.8 18.7 1.0
C A:HIS842 3.9 18.5 1.0
N A:LEU862 3.9 20.0 1.0
N A:ASP840 4.1 18.3 1.0
CA A:HIS843 4.1 18.5 1.0
CA A:SER861 4.2 20.4 1.0
ND1 A:HIS863 4.3 21.2 1.0
N A:GLY844 4.3 18.3 1.0
N A:TRP839 4.3 18.1 1.0
N A:HIS843 4.3 18.4 1.0
C A:SER861 4.3 20.1 1.0
CA A:ASP838 4.4 17.8 1.0
C A:TRP839 4.4 18.4 1.0
N A:HIS863 4.4 20.9 1.0
CA A:ASP840 4.4 18.4 1.0
CA A:HIS863 4.4 21.3 1.0
CA A:TRP839 4.5 18.4 1.0
CG A:HIS863 4.5 21.2 1.0
CA A:LEU862 4.5 19.9 1.0
C A:HIS843 4.5 18.3 1.0
OH A:TYR859 4.6 18.6 1.0
CB A:ASP840 4.6 18.5 1.0
N A:HIS842 4.7 18.5 1.0
C A:VAL841 4.9 18.4 1.0
N A:VAL841 4.9 18.6 1.0
CA A:HIS842 4.9 18.6 1.0

Sodium binding site 2 out of 2 in 5a2s

Go back to Sodium Binding Sites List in 5a2s
Sodium binding site 2 out of 2 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4

b:22.9
occ:1.00
OG B:SER861 2.6 21.7 1.0
O B:ASP840 2.7 19.9 1.0
O B:HIS842 2.7 21.5 1.0
O B:LEU862 2.8 21.4 1.0
O B:ASP838 2.8 19.9 1.0
OD1 B:ASP838 2.9 20.1 1.0
CG B:ASP838 3.4 20.4 1.0
C B:ASP838 3.6 20.1 1.0
C B:LEU862 3.7 21.7 1.0
C B:HIS842 3.7 21.4 1.0
C B:ASP840 3.7 20.1 1.0
CB B:SER861 3.9 22.2 1.0
N B:LEU862 3.9 22.1 1.0
CB B:HIS863 3.9 21.4 1.0
N B:ASP840 3.9 19.3 1.0
OD2 B:ASP838 3.9 20.6 1.0
CB B:ASP838 4.0 20.3 1.0
CA B:HIS843 4.2 21.6 1.0
ND1 B:HIS863 4.2 21.6 1.0
CA B:SER861 4.3 22.0 1.0
CA B:ASP840 4.3 19.9 1.0
N B:HIS843 4.3 21.3 1.0
N B:TRP839 4.3 19.8 1.0
N B:HIS863 4.4 21.3 1.0
C B:TRP839 4.4 19.0 1.0
CA B:HIS863 4.4 21.4 1.0
CA B:ASP838 4.4 20.3 1.0
CA B:TRP839 4.4 19.2 1.0
CA B:LEU862 4.5 21.9 1.0
N B:HIS842 4.5 20.8 1.0
CB B:ASP840 4.5 20.2 1.0
C B:SER861 4.5 22.1 1.0
N B:GLY844 4.5 22.9 1.0
CG B:HIS863 4.5 21.1 1.0
OH B:TYR859 4.6 21.3 1.0
C B:VAL841 4.7 20.7 1.0
CA B:HIS842 4.7 20.9 1.0
C B:HIS843 4.7 22.4 1.0
N B:VAL841 4.8 20.2 1.0
O B:HOH2026 4.9 16.0 1.0
CE1 B:HIS802 4.9 19.9 1.0
ND1 B:HIS802 5.0 20.1 1.0

Reference:

C.A.Luckhurst, P.Breccia, A.J.Stott, O.Aziz, H.L.Birch, R.W.Burli, S.J.Hughes, R.E.Jarvis, M.Lamers, P.M.Leonard, K.L.Matthews, G.Mcallister, S.Pollack, E.Saville-Stones, G.Wishart, D.Yates, C.Dominguez. Potent, Selective, and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors. Acs Med.Chem.Lett. V. 7 34 2016.
ISSN: ISSN 1948-5875
PubMed: 26819662
DOI: 10.1021/ACSMEDCHEMLETT.5B00302
Page generated: Tue Dec 15 10:11:12 2020

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