Sodium in PDB 7zzu: Inhibitory Ligand Binding to HDAC2

All present enzymatic activity of Inhibitory Ligand Binding to HDAC2:
3.5.1.98;

The structure of Inhibitory Ligand Binding to HDAC2, PDB code: 7zzu was solved by A.Cleasby, D.Tisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.35, 98.352, 139.291, 90, 90, 90
R / Rfree (%)	15.4 / 18.2

The structure of Inhibitory Ligand Binding to HDAC2 also contains other interesting chemical elements:

Zinc	(Zn)	3 atoms
Calcium	(Ca)	3 atoms

The binding sites of Sodium atom in the Inhibitory Ligand Binding to HDAC2 (pdb code 7zzu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Inhibitory Ligand Binding to HDAC2, PDB code: 7zzu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Inhibitory Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inhibitory Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na612 b:9.7 occ:1.00 O A:PHE192 2.5 16.1 1.0 O A:HOH747 2.5 15.9 1.0 O A:VAL198 2.6 16.4 1.0 O A:THR195 2.7 16.7 1.0 O A:HOH825 2.8 17.9 1.0 O A:TYR227 3.1 15.7 1.0 C A:PHE192 3.5 15.9 1.0 CB A:TYR227 3.7 18.0 1.0 C A:TYR227 3.8 16.3 1.0 C A:VAL198 3.8 15.7 1.0 C A:THR195 3.9 18.8 1.0 CB A:PHE192 4.1 14.9 1.0 CA A:TYR193 4.3 16.3 1.0 N A:TYR193 4.3 15.9 1.0 CA A:TYR227 4.3 17.3 1.0 C A:TYR193 4.4 17.5 1.0 CA A:PHE192 4.4 14.9 1.0 N A:THR195 4.4 18.4 1.0 O A:TYR193 4.5 17.5 1.0 CA A:MET199 4.5 16.0 1.0 CG2 A:THR195 4.5 18.3 1.0 N A:ALA228 4.6 15.2 1.0 N A:MET199 4.6 14.7 1.0 N A:THR200 4.6 13.4 1.0 O A:GLY224 4.7 18.4 1.0 CA A:THR195 4.7 19.6 1.0 CA A:VAL198 4.7 15.5 1.0 CA A:GLY224 4.8 20.5 1.0 OG1 A:THR200 4.8 13.7 1.0 CB A:VAL198 4.9 14.6 1.0 N A:VAL198 4.9 16.3 1.0 N A:ASP196 5.0 19.6 1.0 N A:THR194 5.0 18.2 1.0

Sodium binding site 2 out of 3 in the Inhibitory Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inhibitory Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na609 b:11.7 occ:1.00 O B:PHE192 2.4 16.6 1.0 O B:HOH767 2.4 16.8 1.0 O B:VAL198 2.5 18.1 1.0 O B:THR195 2.8 18.2 1.0 O B:HOH800 2.9 24.0 1.0 O B:TYR227 3.3 16.3 1.0 C B:PHE192 3.5 17.0 1.0 C B:VAL198 3.7 16.9 1.0 CB B:TYR227 3.7 17.4 1.0 C B:TYR227 3.9 16.9 1.0 C B:THR195 4.0 19.3 1.0 CB B:PHE192 4.0 15.1 1.0 CA B:TYR193 4.3 17.8 1.0 N B:TYR193 4.3 17.4 1.0 CA B:PHE192 4.4 16.0 1.0 C B:TYR193 4.4 18.6 1.0 N B:THR195 4.4 20.9 1.0 O B:TYR193 4.4 19.6 1.0 CA B:TYR227 4.4 17.7 1.0 CA B:MET199 4.5 16.6 1.0 CG2 B:THR195 4.5 19.5 1.0 N B:MET199 4.6 16.6 1.0 N B:ALA228 4.7 16.4 1.0 O B:GLY224 4.7 19.1 1.0 CA B:GLY224 4.7 21.5 1.0 N B:THR200 4.7 14.2 1.0 CA B:VAL198 4.7 15.9 1.0 CA B:THR195 4.7 20.9 1.0 OG1 B:THR200 4.8 15.2 1.0 N B:VAL198 4.8 16.6 1.0 CB B:VAL198 4.8 14.8 1.0 N B:THR194 4.9 19.4 1.0 N B:ASP196 5.0 20.3 1.0 CG B:TYR227 5.0 18.7 1.0

Sodium binding site 3 out of 3 in the Inhibitory Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Inhibitory Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na605 b:14.1 occ:1.00 O C:PHE192 2.5 16.9 1.0 O C:HOH745 2.5 20.2 1.0 O C:VAL198 2.5 19.7 1.0 O C:THR195 2.8 18.9 1.0 O C:HOH759 2.9 23.1 1.0 O C:TYR227 3.2 19.7 1.0 C C:PHE192 3.5 17.5 1.0 CB C:TYR227 3.7 20.7 1.0 C C:VAL198 3.7 20.5 1.0 C C:TYR227 3.8 20.3 1.0 C C:THR195 4.0 19.6 1.0 CB C:PHE192 4.1 17.9 1.0 CA C:TYR227 4.3 20.8 1.0 CA C:TYR193 4.4 18.0 1.0 N C:TYR193 4.4 17.4 1.0 CA C:MET199 4.4 21.4 1.0 C C:TYR193 4.4 18.4 1.0 O C:TYR193 4.4 18.6 1.0 CA C:PHE192 4.4 17.3 1.0 N C:THR195 4.5 18.5 1.0 CG2 C:THR195 4.5 18.4 1.0 N C:MET199 4.5 20.0 1.0 N C:ALA228 4.5 20.5 1.0 N C:THR200 4.6 19.6 1.0 O C:GLY224 4.7 20.9 1.0 CA C:VAL198 4.7 19.6 1.0 CA C:GLY224 4.8 21.5 1.0 CA C:THR195 4.8 19.3 1.0 OG1 C:THR200 4.8 18.4 1.0 CB C:VAL198 4.9 18.6 1.0 N C:VAL198 4.9 19.5 1.0 C C:MET199 5.0 20.3 1.0 N C:THR194 5.0 18.0 1.0 CG2 C:THR200 5.0 18.9 1.0 CG C:TYR227 5.0 21.5 1.0

E.Tamanini, S.Miyamura, I.M.Buck, B.D.Cons, L.Dawson, C.East, T.Futamura, S.Goto, C.Griffiths-Jones, T.Hashimoto, T.D.Heightman, S.Ishikawa, H.Ito, Y.Kaneko, T.Kawato, K.Kondo, N.Kurihara, J.M.Mccarthy, Y.Mori, T.Nagase, Y.Nakaishi, J.Reeks, A.Sato, P.Schopf, K.Tai, T.Tamai, D.Tisi, A.J.Woolford. Fragment-Based Discovery of A Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. Acs Med.Chem.Lett. V. 13 1591 2022.
ISSN: ISSN 1948-5875
PubMed: 36262388
DOI: 10.1021/ACSMEDCHEMLETT.2C00272