Zinc in PDB 7zzt: Ligand Binding to HDAC2

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

The structure of Ligand Binding to HDAC2, PDB code: 7zzt 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)	48.39 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.208, 98.023, 139.275, 90, 90, 90
R / Rfree (%)	14.8 / 17.3

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

Calcium	(Ca)	3 atoms
Sodium	(Na)	3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:14.8 occ:1.00 H18 A:KJF607 1.7 13.8 1.0 H20 A:KJF607 1.7 13.8 1.0 OD2 A:ASP181 2.0 13.5 1.0 OD2 A:ASP269 2.0 13.2 1.0 ND1 A:HIS183 2.1 16.1 1.0 N1 A:KJF607 2.1 14.1 1.0 O12 A:KJF607 2.5 15.5 1.0 H19 A:KJF607 2.8 14.0 1.0 CG A:ASP181 2.8 12.9 1.0 CG A:ASP269 2.9 14.5 1.0 CE1 A:HIS183 2.9 14.9 1.0 OD1 A:ASP181 3.0 12.6 1.0 C11 A:KJF607 3.0 15.1 1.0 C2 A:KJF607 3.1 14.2 1.0 CG A:HIS183 3.2 14.8 1.0 OD1 A:ASP269 3.3 14.8 1.0 CB A:HIS183 3.6 14.9 1.0 H21 A:KJF607 3.6 14.3 1.0 N A:HIS183 3.9 14.8 1.0 CA A:GLY306 4.0 14.9 1.0 CG2 A:ILE182 4.1 16.3 1.0 N13 A:KJF607 4.1 15.2 1.0 NE2 A:HIS183 4.1 16.0 1.0 NE2 A:HIS145 4.1 15.6 1.0 H22 A:KJF607 4.1 14.8 1.0 CB A:ASP269 4.2 13.4 1.0 CD2 A:HIS183 4.2 16.0 1.0 C3 A:KJF607 4.2 14.8 1.0 CB A:ASP181 4.2 13.1 1.0 N A:GLY306 4.2 14.0 1.0 CA A:HIS183 4.4 14.3 1.0 N A:ILE182 4.5 13.5 1.0 H31 A:KJF607 4.5 16.6 1.0 CE1 A:HIS145 4.6 16.2 1.0 H25 A:KJF607 4.7 15.1 1.0 C A:ILE182 4.8 14.4 1.0 C14 A:KJF607 4.9 16.7 1.0 NE2 A:HIS146 4.9 16.2 1.0 H37 A:KJF607 4.9 16.6 1.0 H23 A:KJF607 4.9 14.7 1.0 C A:ASP181 4.9 13.8 1.0 CA A:ASP181 4.9 13.4 1.0 C A:GLY306 5.0 15.4 1.0 OH A:TYR308 5.0 17.2 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:13.4 occ:1.00 H18 B:KJF610 1.7 13.6 1.0 H20 B:KJF610 1.8 13.5 1.0 OD2 B:ASP269 2.0 13.2 1.0 ND1 B:HIS183 2.0 14.2 1.0 OD2 B:ASP181 2.0 12.0 1.0 N1 B:KJF610 2.1 13.6 1.0 O12 B:KJF610 2.5 14.1 1.0 H19 B:KJF610 2.8 13.6 1.0 CG B:ASP181 2.8 12.1 1.0 CE1 B:HIS183 2.9 13.8 1.0 CG B:ASP269 2.9 14.3 1.0 C11 B:KJF610 3.0 15.1 1.0 OD1 B:ASP181 3.0 12.6 1.0 C2 B:KJF610 3.1 14.1 1.0 CG B:HIS183 3.1 13.7 1.0 OD1 B:ASP269 3.3 12.6 1.0 CB B:HIS183 3.6 13.7 1.0 H21 B:KJF610 3.6 13.9 1.0 N B:HIS183 3.9 13.1 1.0 NE2 B:HIS183 4.1 14.8 1.0 N13 B:KJF610 4.1 14.5 1.0 H22 B:KJF610 4.1 14.2 1.0 CA B:GLY306 4.1 13.5 1.0 CD2 B:HIS183 4.2 16.1 1.0 NE2 B:HIS145 4.2 12.7 1.0 CG2 B:ILE182 4.2 14.1 1.0 C3 B:KJF610 4.2 13.8 1.0 CB B:ASP181 4.2 12.0 1.0 CB B:ASP269 4.2 12.5 1.0 N B:GLY306 4.3 12.7 1.0 CA B:HIS183 4.4 13.7 1.0 N B:ILE182 4.4 12.5 1.0 H31 B:KJF610 4.5 15.8 1.0 CE1 B:HIS145 4.6 13.3 1.0 H25 B:KJF610 4.7 14.6 1.0 C14 B:KJF610 4.9 16.4 1.0 C B:ILE182 4.9 13.8 1.0 NE2 B:HIS146 4.9 14.4 1.0 H23 B:KJF610 4.9 14.2 1.0 H37 B:KJF610 4.9 14.4 1.0 CA B:ASP181 4.9 12.8 1.0 CE1 B:TYR308 5.0 13.1 1.0 C B:ASP181 5.0 13.3 1.0 OH B:TYR308 5.0 14.5 1.0

Zinc binding site 3 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:18.1 occ:1.00 H18 C:KJF605 1.7 14.4 0.8 H20 C:KJF605 1.8 14.3 0.8 OD2 C:ASP269 2.0 16.9 1.0 OD2 C:ASP181 2.0 16.0 1.0 ND1 C:HIS183 2.1 17.9 1.0 N1 C:KJF605 2.1 14.3 0.8 O12 C:KJF605 2.5 17.3 0.8 CG C:ASP181 2.8 17.2 1.0 H19 C:KJF605 2.8 14.4 0.8 CG C:ASP269 2.9 17.5 1.0 OD1 C:ASP181 3.0 18.6 1.0 CE1 C:HIS183 3.0 18.9 1.0 C11 C:KJF605 3.0 16.8 0.8 C2 C:KJF605 3.1 15.3 0.8 CG C:HIS183 3.2 18.4 1.0 OD1 C:ASP269 3.3 17.5 1.0 CB C:HIS183 3.6 17.6 1.0 H21 C:KJF605 3.6 14.9 0.8 N C:HIS183 3.9 17.0 1.0 CA C:GLY306 4.0 17.9 1.0 N13 C:KJF605 4.1 16.2 0.8 H22 C:KJF605 4.1 14.3 0.8 CG2 C:ILE182 4.1 19.4 1.0 NE2 C:HIS183 4.1 19.3 1.0 NE2 C:HIS145 4.2 18.0 1.0 C3 C:KJF605 4.2 13.8 0.8 CB C:ASP181 4.2 16.5 1.0 CB C:ASP269 4.2 18.1 1.0 CD2 C:HIS183 4.3 20.3 1.0 N C:GLY306 4.3 17.8 1.0 N C:ILE182 4.4 17.7 1.0 CA C:HIS183 4.4 17.0 1.0 H31 C:KJF605 4.5 17.2 0.8 CE1 C:HIS145 4.6 18.5 1.0 H25 C:KJF605 4.7 14.4 0.8 C C:ILE182 4.8 17.9 1.0 C14 C:KJF605 4.8 17.3 0.8 NE2 C:HIS146 4.9 18.0 1.0 H37 C:KJF605 4.9 16.6 0.8 C C:ASP181 4.9 17.6 1.0 H23 C:KJF605 4.9 14.3 0.8 CA C:ASP181 4.9 17.7 1.0 CE1 C:TYR308 5.0 19.5 1.0 CA C:ILE182 5.0 18.1 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