Zinc in PDB 7zzo: HDAC2 in Complex with An Inhibitor

All present enzymatic activity of HDAC2 in Complex with An Inhibitor:
3.5.1.98;

The structure of HDAC2 in Complex with An Inhibitor, PDB code: 7zzo 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)	79.80 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.079, 97.444, 139.049, 90, 90, 90
R / Rfree (%)	17.2 / 22.5

The structure of HDAC2 in Complex with An Inhibitor also contains other interesting chemical elements:

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

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

Zinc binding site 1 out of 3 in the HDAC2 in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC2 in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:14.0 occ:1.00 H18 A:KIZ604 1.6 11.7 0.9 H19 A:KIZ604 1.7 12.3 0.9 OD2 A:ASP181 1.9 11.5 1.0 N7 A:KIZ604 2.0 12.9 0.9 OD2 A:ASP269 2.0 12.8 1.0 ND1 A:HIS183 2.0 14.8 1.0 O5 A:KIZ604 2.7 12.2 0.9 H17 A:KIZ604 2.7 12.5 0.9 CG A:ASP181 2.8 11.4 1.0 C6 A:KIZ604 2.9 13.2 0.9 CG A:ASP269 2.9 12.4 1.0 CE1 A:HIS183 2.9 15.7 1.0 C4 A:KIZ604 3.0 15.2 0.9 OD1 A:ASP181 3.0 11.1 1.0 CG A:HIS183 3.1 14.8 1.0 H16 A:KIZ604 3.1 14.4 0.9 OD1 A:ASP269 3.2 11.3 1.0 CB A:HIS183 3.5 14.4 1.0 N A:HIS183 3.8 13.4 1.0 CA A:GLY306 4.0 12.8 1.0 CG2 A:ILE182 4.1 14.0 1.0 N2 A:KIZ604 4.1 19.1 0.9 NE2 A:HIS183 4.1 16.0 1.0 NE2 A:HIS145 4.2 12.4 1.0 CD2 A:HIS183 4.2 15.8 1.0 CB A:ASP181 4.2 11.0 1.0 CB A:ASP269 4.3 12.9 1.0 C8 A:KIZ604 4.3 18.3 0.9 N A:GLY306 4.3 12.5 1.0 CA A:HIS183 4.3 14.2 1.0 N A:ILE182 4.4 12.1 1.0 CE1 A:HIS145 4.6 12.4 1.0 H23 A:KIZ604 4.6 21.1 0.9 H27 A:KIZ604 4.6 16.1 0.9 C9 A:KIZ604 4.7 17.5 0.9 H20 A:KIZ604 4.7 19.0 0.9 C A:ILE182 4.8 13.2 1.0 C3 A:KIZ604 4.8 22.4 0.9 CE1 A:TYR308 4.9 16.6 1.0 CA A:ASP181 4.9 10.8 1.0 H26 A:KIZ604 4.9 16.3 0.9 C A:ASP181 4.9 11.5 1.0 OH A:TYR308 5.0 16.1 1.0 C A:GLY306 5.0 13.2 1.0 C1 A:KIZ604 5.0 19.8 0.9

Zinc binding site 2 out of 3 in the HDAC2 in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HDAC2 in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:12.9 occ:1.00 H19 B:KIZ606 1.6 12.5 0.8 H18 B:KIZ606 1.9 12.9 0.8 OD2 B:ASP269 1.9 11.5 1.0 OD2 B:ASP181 2.0 10.7 1.0 ND1 B:HIS183 2.0 11.6 1.0 N7 B:KIZ606 2.0 12.7 0.8 H17 B:KIZ606 2.8 13.1 0.8 CG B:ASP181 2.8 10.8 1.0 O5 B:KIZ606 2.8 10.0 0.8 CE1 B:HIS183 2.8 12.9 1.0 CG B:ASP269 2.8 11.6 1.0 C6 B:KIZ606 2.9 14.7 0.8 OD1 B:ASP181 3.0 10.2 1.0 C4 B:KIZ606 3.1 12.9 0.8 CG B:HIS183 3.1 12.3 1.0 H16 B:KIZ606 3.1 14.4 0.8 OD1 B:ASP269 3.2 11.1 1.0 CB B:HIS183 3.5 12.4 1.0 N B:HIS183 3.8 11.3 1.0 NE2 B:HIS183 4.0 13.3 1.0 CA B:GLY306 4.0 11.3 1.0 CG2 B:ILE182 4.1 12.0 1.0 NE2 B:HIS145 4.1 12.0 1.0 CD2 B:HIS183 4.2 13.7 1.0 N2 B:KIZ606 4.2 14.1 0.8 CB B:ASP181 4.2 10.7 1.0 CB B:ASP269 4.2 11.1 1.0 N B:GLY306 4.3 10.9 1.0 C8 B:KIZ606 4.3 17.6 0.8 CA B:HIS183 4.3 12.0 1.0 N B:ILE182 4.4 10.8 1.0 CE1 B:HIS145 4.6 11.0 1.0 H23 B:KIZ606 4.6 13.6 0.8 H27 B:KIZ606 4.7 16.6 0.8 C9 B:KIZ606 4.7 17.9 0.8 H20 B:KIZ606 4.8 15.9 0.8 C B:ILE182 4.8 11.9 1.0 CE1 B:TYR308 4.9 12.8 1.0 CA B:ASP181 4.9 10.7 1.0 C B:ASP181 4.9 11.2 1.0 C1 B:KIZ606 5.0 17.3 0.8 H26 B:KIZ606 5.0 16.4 0.8 CA B:ILE182 5.0 11.5 1.0

Zinc binding site 3 out of 3 in the HDAC2 in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HDAC2 in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:20.0 occ:1.00 H19 C:KIZ605 1.6 14.0 0.8 H18 C:KIZ605 1.8 15.0 0.8 OD2 C:ASP269 1.9 20.3 1.0 OD2 C:ASP181 2.0 17.8 1.0 ND1 C:HIS183 2.1 21.8 1.0 N7 C:KIZ605 2.1 16.3 0.8 CG C:ASP181 2.8 18.1 1.0 H17 C:KIZ605 2.8 15.3 0.8 O5 C:KIZ605 2.8 18.8 0.8 CG C:ASP269 2.9 20.3 1.0 OD1 C:ASP181 2.9 17.6 1.0 CE1 C:HIS183 3.0 23.1 1.0 C6 C:KIZ605 3.0 16.1 0.8 C4 C:KIZ605 3.1 17.8 0.8 CG C:HIS183 3.1 21.7 1.0 OD1 C:ASP269 3.2 19.7 1.0 H16 C:KIZ605 3.2 16.4 0.8 CB C:HIS183 3.5 20.2 1.0 N C:HIS183 3.8 19.9 1.0 CG2 C:ILE182 4.0 21.7 1.0 CA C:GLY306 4.0 22.0 1.0 NE2 C:HIS183 4.1 23.3 1.0 N2 C:KIZ605 4.1 19.2 0.8 NE2 C:HIS145 4.2 18.8 1.0 CB C:ASP181 4.2 17.9 1.0 CD2 C:HIS183 4.2 23.1 1.0 CB C:ASP269 4.2 21.5 1.0 N C:ILE182 4.3 20.4 1.0 CA C:HIS183 4.3 20.1 1.0 N C:GLY306 4.3 21.0 1.0 C8 C:KIZ605 4.3 16.5 0.8 CE1 C:HIS145 4.6 18.4 1.0 H23 C:KIZ605 4.7 19.6 0.8 H27 C:KIZ605 4.7 15.5 0.8 H20 C:KIZ605 4.7 21.7 0.8 C C:ILE182 4.8 20.5 1.0 C9 C:KIZ605 4.8 15.8 0.8 C3 C:KIZ605 4.9 21.2 0.8 C C:ASP181 4.9 19.4 1.0 CA C:ILE182 4.9 20.9 1.0 CA C:ASP181 4.9 19.0 1.0 CE1 C:TYR308 5.0 24.5 1.0 C C:GLY306 5.0 23.2 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