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Sodium in PDB 4cby: Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease

Enzymatic activity of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease

All present enzymatic activity of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease:
3.5.1.98;

Protein crystallography data

The structure of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease, PDB code: 4cby was solved by R.W.Burli, C.A.Luckhurst, O.Aziz, K.L.Matthews, D.Yates, K.A.Lyons, M.Beconi, G.Mcallister, P.Breccia, A.J.Stott, S.D.Penrose, M.Wall, M.Lamers, P.Leonard, I.Mueller, C.M.Richardson, R.Jarvis, L.Stones, S.Hughes, G.Wishart, A.F.Haughan, C.Oconnell, T.Mead, H.Mcneil, J.Vann, J.Mangette, M.Maillard, V.Beaumont, I.Munoz-Sanjuan, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.1 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.151, 161.816, 83.732, 90.00, 97.03, 90.00
R / Rfree (%) 20.907 / 24.592

Other elements in 4cby:

The structure of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease (pdb code 4cby). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease, PDB code: 4cby:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 1 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2036

b:28.3
occ:1.00
 O A:ASP838 2.3 26.0 1.0
OD1 A:ASP838 2.3 32.0 1.0
OG A:SER861 2.5 27.4 1.0
O A:ASP840 2.7 20.9 1.0
CG A:ASP838 2.8 30.3 1.0
O A:LEU862 3.0 25.8 1.0
C A:ASP838 3.1 24.0 1.0
O A:HIS842 3.1 23.1 1.0
CB A:ASP838 3.5 27.1 1.0
OD2 A:ASP838 3.5 32.7 1.0
CB A:SER861 3.6 27.8 1.0
N A:ASP840 3.7 20.5 1.0
C A:ASP840 3.7 20.6 1.0
CA A:ASP838 3.8 25.1 1.0
N A:TRP839 3.9 22.1 1.0
C A:LEU862 3.9 25.5 1.0
N A:LEU862 4.0 27.4 1.0
CA A:SER861 4.0 27.8 1.0
C A:HIS842 4.1 22.4 1.0
CA A:TRP839 4.1 21.2 1.0
C A:TRP839 4.1 20.6 1.0
CB A:HIS863 4.1 25.2 1.0
CA A:ASP840 4.2 20.2 1.0
CB A:ASP840 4.3 19.9 1.0
C A:SER861 4.4 27.7 1.0
CA A:HIS843 4.5 20.4 1.0
ND1 A:HIS863 4.6 24.2 1.0
CA A:LEU862 4.6 25.5 1.0
OH A:TYR859 4.6 27.7 1.0
N A:GLY844 4.7 21.3 1.0
N A:HIS863 4.7 25.5 1.0
N A:HIS843 4.7 21.1 1.0
CA A:HIS863 4.8 25.9 1.0
CG A:HIS863 4.8 24.7 1.0
N A:HIS842 4.8 21.6 1.0
O A:HOH2010 4.9 20.1 1.0
N A:VAL841 4.9 20.7 1.0
C A:HIS843 4.9 20.9 1.0
N A:ASP838 4.9 24.1 1.0
O A:TRP839 5.0 19.7 1.0
CE1 A:HIS802 5.0 25.1 1.0
C A:VAL841 5.0 21.5 1.0

Sodium binding site 2 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 2 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2037

b:20.4
occ:1.00
 O A:ASP854 2.3 20.7 1.0
O A:PHE851 2.3 20.2 1.0
O A:VAL857 2.3 23.7 1.0
O A:PHE888 3.4 16.9 1.0
C A:PHE851 3.4 20.2 1.0
C A:ASP854 3.4 20.2 1.0
C A:VAL857 3.5 23.0 1.0
CB A:PHE888 3.8 16.3 1.0
CB A:PHE851 3.8 20.7 1.0
C A:PHE888 4.0 17.2 1.0
N A:ASP854 4.1 20.8 1.0
CA A:ASP854 4.2 20.5 1.0
CA A:PHE851 4.2 20.4 1.0
N A:TYR852 4.4 20.5 1.0
CB A:ASP854 4.4 20.5 1.0
N A:PRO855 4.5 20.1 1.0
N A:LEU858 4.5 23.1 1.0
CA A:VAL857 4.5 22.1 1.0
C A:TYR852 4.5 20.1 1.0
CA A:PHE888 4.5 16.7 1.0
CB A:VAL857 4.6 21.2 1.0
CA A:TYR852 4.6 20.1 1.0
CA A:LEU858 4.6 22.7 1.0
O A:TYR852 4.6 20.3 1.0
N A:VAL857 4.6 22.6 1.0
CA A:PRO855 4.6 20.3 1.0
O A:GLY885 4.8 15.2 1.0
N A:ASN889 4.8 17.9 1.0
N A:SER853 4.9 20.6 1.0
N A:TYR859 5.0 25.4 1.0

Sodium binding site 3 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 3 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2035

b:28.8
occ:1.00
 O B:ASP838 2.3 24.9 1.0
OD1 B:ASP838 2.3 26.9 1.0
OG B:SER861 2.5 33.5 1.0
O B:ASP840 2.6 20.0 1.0
CG B:ASP838 2.9 25.1 1.0
O B:LEU862 2.9 30.9 1.0
C B:ASP838 3.1 23.4 1.0
O B:HIS842 3.1 21.1 1.0
CB B:ASP838 3.5 24.3 1.0
OD2 B:ASP838 3.6 25.9 1.0
CB B:SER861 3.7 32.9 1.0
C B:ASP840 3.7 20.7 1.0
N B:ASP840 3.7 21.3 1.0
C B:LEU862 3.8 30.2 1.0
N B:TRP839 3.8 22.2 1.0
CA B:ASP838 3.9 23.8 1.0
N B:LEU862 3.9 31.2 1.0
CA B:SER861 4.0 31.7 1.0
CA B:TRP839 4.1 22.0 1.0
C B:TRP839 4.1 21.9 1.0
CB B:HIS863 4.1 32.9 1.0
C B:HIS842 4.1 21.2 1.0
CA B:ASP840 4.1 20.6 1.0
C B:SER861 4.3 31.9 1.0
CB B:ASP840 4.3 20.5 1.0
CA B:HIS843 4.5 22.7 1.0
ND1 B:HIS863 4.5 34.9 1.0
CA B:LEU862 4.6 29.4 1.0
N B:HIS863 4.6 30.9 1.0
N B:HIS843 4.7 22.0 1.0
CA B:HIS863 4.7 32.3 1.0
OH B:TYR859 4.7 25.0 1.0
N B:GLY844 4.8 22.9 1.0
N B:HIS842 4.8 21.2 1.0
CG B:HIS863 4.8 33.5 1.0
N B:VAL841 4.8 21.1 1.0
O B:TRP839 4.9 21.3 1.0
C B:VAL841 4.9 21.0 1.0
N B:ASP838 5.0 23.3 1.0
C B:HIS843 5.0 22.4 1.0

Sodium binding site 4 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 4 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2036

b:23.8
occ:1.00
 O B:ASP854 2.3 24.1 1.0
O B:VAL857 2.3 24.3 1.0
O B:PHE851 2.3 24.5 1.0
O B:HOH2014 2.5 24.1 1.0
O B:PHE888 3.3 28.7 1.0
C B:PHE851 3.4 25.4 1.0
C B:ASP854 3.4 23.9 1.0
C B:VAL857 3.5 24.1 1.0
CB B:PHE888 3.8 29.9 1.0
CB B:PHE851 3.8 25.1 1.0
C B:PHE888 4.0 28.4 1.0
N B:ASP854 4.1 24.8 1.0
CA B:ASP854 4.2 24.0 1.0
CA B:PHE851 4.3 25.0 1.0
N B:TYR852 4.4 25.9 1.0
CB B:ASP854 4.4 24.1 1.0
N B:LEU858 4.4 23.9 1.0
N B:PRO855 4.5 24.2 1.0
CA B:VAL857 4.5 23.6 1.0
CA B:PHE888 4.5 29.2 1.0
C B:TYR852 4.5 26.0 1.0
CA B:LEU858 4.6 23.9 1.0
CB B:VAL857 4.6 23.2 1.0
N B:VAL857 4.6 23.9 1.0
CA B:TYR852 4.6 25.6 1.0
O B:TYR852 4.6 29.1 1.0
CA B:PRO855 4.6 23.8 1.0
O B:GLY885 4.8 39.6 1.0
N B:ASN889 4.8 26.7 1.0
N B:TYR859 4.9 26.7 1.0
N B:SER853 5.0 26.1 1.0

Sodium binding site 5 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 5 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2036

b:25.8
occ:1.00
 O C:ASP838 2.3 25.5 1.0
OD1 C:ASP838 2.3 25.5 1.0
OG C:SER861 2.4 28.0 1.0
O C:ASP840 2.7 22.2 1.0
CG C:ASP838 2.8 25.3 1.0
O C:LEU862 3.0 23.7 1.0
C C:ASP838 3.1 23.8 1.0
O C:HIS842 3.1 21.9 1.0
CB C:ASP838 3.5 24.6 1.0
OD2 C:ASP838 3.5 25.7 1.0
CB C:SER861 3.6 27.5 1.0
N C:ASP840 3.7 22.5 1.0
C C:ASP840 3.7 22.2 1.0
CA C:ASP838 3.9 23.9 1.0
C C:LEU862 3.9 24.3 1.0
N C:TRP839 3.9 22.5 1.0
N C:LEU862 4.0 25.1 1.0
CA C:SER861 4.0 26.9 1.0
CA C:TRP839 4.1 22.0 1.0
C C:HIS842 4.1 21.9 1.0
C C:TRP839 4.1 21.7 1.0
CB C:HIS863 4.1 23.7 1.0
CA C:ASP840 4.2 22.4 1.0
C C:SER861 4.3 26.2 1.0
CB C:ASP840 4.4 22.9 1.0
CA C:HIS843 4.5 22.3 1.0
ND1 C:HIS863 4.5 22.5 1.0
CA C:LEU862 4.6 24.0 1.0
OH C:TYR859 4.6 23.5 1.0
N C:HIS863 4.7 24.0 1.0
N C:GLY844 4.7 21.7 1.0
N C:HIS843 4.7 22.1 1.0
CA C:HIS863 4.7 24.2 1.0
CG C:HIS863 4.8 23.0 1.0
O C:HOH2014 4.8 21.6 1.0
N C:HIS842 4.8 20.3 1.0
N C:VAL841 4.9 21.3 1.0
C C:HIS843 4.9 22.1 1.0
N C:ASP838 4.9 23.4 1.0
O C:TRP839 5.0 19.8 1.0
C C:VAL841 5.0 19.9 1.0

Sodium binding site 6 out of 8 in 4cby

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Sodium binding site 6 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2037

b:22.4
occ:1.00
 O C:VAL857 2.2 24.6 1.0
O C:ASP854 2.3 21.1 1.0
O C:PHE851 2.3 18.7 1.0
O C:HOH2015 2.3 15.0 1.0
O C:PHE888 3.4 21.0 1.0
C C:PHE851 3.4 18.5 1.0
C C:ASP854 3.4 21.3 1.0
C C:VAL857 3.5 24.4 1.0
CB C:PHE888 3.8 20.7 1.0
CB C:PHE851 3.8 19.9 1.0
C C:PHE888 4.0 20.1 1.0
N C:ASP854 4.1 21.2 1.0
CA C:ASP854 4.2 21.0 1.0
CA C:PHE851 4.2 18.9 1.0
N C:TYR852 4.4 18.9 1.0
N C:LEU858 4.4 23.7 1.0
N C:PRO855 4.4 21.8 1.0
CB C:ASP854 4.4 20.7 1.0
CA C:VAL857 4.4 24.3 1.0
CA C:LEU858 4.5 23.1 1.0
C C:TYR852 4.6 18.9 1.0
CA C:PHE888 4.6 20.1 1.0
CB C:VAL857 4.6 25.3 1.0
N C:VAL857 4.6 24.6 1.0
CA C:TYR852 4.6 18.4 1.0
CA C:PRO855 4.6 22.1 1.0
O C:TYR852 4.6 20.1 1.0
O C:GLY885 4.8 19.4 1.0
N C:ASN889 4.9 20.2 1.0
N C:TYR859 4.9 24.0 1.0
N C:SER853 5.0 19.6 1.0

Sodium binding site 7 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 7 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2039

b:23.1
occ:1.00
 O D:ASP838 2.3 22.0 1.0
OD1 D:ASP838 2.3 23.8 1.0
OG D:SER861 2.4 24.7 1.0
O D:ASP840 2.7 21.0 1.0
CG D:ASP838 2.8 23.2 1.0
O D:LEU862 3.0 22.7 1.0
C D:ASP838 3.1 21.5 1.0
O D:HIS842 3.1 24.5 1.0
CB D:ASP838 3.5 22.0 1.0
OD2 D:ASP838 3.5 23.2 1.0
CB D:SER861 3.6 25.2 1.0
N D:ASP840 3.7 20.6 1.0
C D:ASP840 3.7 21.3 1.0
C D:LEU862 3.9 23.4 1.0
CA D:ASP838 3.9 21.5 1.0
N D:TRP839 3.9 20.7 1.0
N D:LEU862 4.0 24.1 1.0
CA D:SER861 4.0 25.4 1.0
C D:HIS842 4.1 24.7 1.0
CB D:HIS863 4.1 22.5 1.0
CA D:TRP839 4.1 20.7 1.0
C D:TRP839 4.1 20.9 1.0
CA D:ASP840 4.2 20.9 1.0
C D:SER861 4.4 24.9 1.0
CB D:ASP840 4.4 21.2 1.0
CA D:HIS843 4.5 25.1 1.0
ND1 D:HIS863 4.5 22.7 1.0
CA D:LEU862 4.6 23.5 1.0
OH D:TYR859 4.6 20.7 1.0
N D:HIS863 4.6 23.1 1.0
O D:HOH2012 4.7 19.1 1.0
N D:HIS843 4.7 25.4 1.0
N D:GLY844 4.7 23.5 1.0
CA D:HIS863 4.7 23.1 1.0
CG D:HIS863 4.8 22.3 1.0
N D:HIS842 4.8 22.8 1.0
N D:VAL841 4.9 21.8 1.0
C D:HIS843 4.9 23.6 1.0
N D:ASP838 4.9 21.7 1.0
CE1 D:HIS802 5.0 24.4 1.0
C D:VAL841 5.0 22.1 1.0
O D:TRP839 5.0 21.6 1.0

Sodium binding site 8 out of 8 in 4cby

Go back to Sodium Binding Sites List in 4cby
Sodium binding site 8 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2040

b:24.5
occ:1.00
 O D:VAL857 2.3 24.1 1.0
O D:ASP854 2.3 22.6 1.0
O D:PHE851 2.3 21.3 1.0
O D:HOH2014 2.6 19.2 1.0
O D:PHE888 3.3 25.6 1.0
C D:ASP854 3.4 21.8 1.0
C D:PHE851 3.4 21.3 1.0
C D:VAL857 3.5 22.8 1.0
CB D:PHE888 3.8 25.4 1.0
CB D:PHE851 3.9 20.9 1.0
C D:PHE888 4.0 25.3 1.0
N D:ASP854 4.1 21.5 1.0
CA D:ASP854 4.2 21.0 1.0
CA D:PHE851 4.3 21.1 1.0
N D:TYR852 4.4 21.5 1.0
N D:LEU858 4.4 23.4 1.0
N D:PRO855 4.4 21.8 1.0
CA D:VAL857 4.5 22.0 1.0
CB D:ASP854 4.5 20.5 1.0
CA D:PHE888 4.5 25.3 1.0
CA D:LEU858 4.5 23.6 1.0
C D:TYR852 4.5 20.3 1.0
CB D:VAL857 4.6 22.4 1.0
N D:VAL857 4.6 21.6 1.0
CA D:TYR852 4.6 20.9 1.0
O D:TYR852 4.6 20.7 1.0
CA D:PRO855 4.6 21.1 1.0
O D:GLY885 4.8 23.8 1.0
N D:ASN889 4.8 23.2 1.0
N D:TYR859 4.9 23.4 1.0
N D:SER853 5.0 20.5 1.0
CG D:PHE888 5.0 25.6 1.0

Reference:

R.W.Burli, C.A.Luckhurst, O.Aziz, K.L.Matthews, D.Yates, K.A.Lyons, M.Beconi, G.Mcallister, P.Breccia, A.J.Stott, S.D.Penrose, M.Wall, M.B.A.C.Lamers, P.Leonard, I.Mueller, C.M.Richardson, R.Jarvis, L.Stones, S.Hughes, G.Wishart, A.F.Haughan, C.O'connell, T.Mead, H.Mcneil, J.Vann, J.Mangette, M.Maillard, V.Beaumont, I.Munoz-Sanjuan, C.Dominguez. Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Histone Deacetylase (Hdac) Inhibitors As A Potential Therapy For Huntington'S Disease. J.Med.Chem. V. 56 9934 2013.
ISSN: ISSN 0022-2623
PubMed: 24261862
DOI: 10.1021/JM4011884
Page generated: Mon Oct 7 14:40:58 2024

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