Zinc in PDB 8a0b: Inhibitor Binding to HDAC2

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

The structure of Inhibitor Binding to HDAC2, PDB code: 8a0b 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)	67.17 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.221, 98.018, 139.402, 90, 90, 90
R / Rfree (%)	16.5 / 18.8

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

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

The binding sites of Zinc atom in the Inhibitor Binding to HDAC2 (pdb code 8a0b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Inhibitor Binding to HDAC2, PDB code: 8a0b:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Inhibitor 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 Inhibitor Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:21.2 occ:1.00 H25 A:KRU605 1.3 20.6 1.0 OD2 A:ASP269 2.0 20.5 1.0 OD2 A:ASP181 2.0 19.3 1.0 ND1 A:HIS183 2.0 21.8 1.0 N7 A:KRU605 2.1 20.7 1.0 H26 A:KRU605 2.5 20.7 1.0 O1 A:KRU605 2.5 19.6 1.0 CG A:ASP181 2.8 18.8 1.0 CE1 A:HIS183 2.9 22.0 1.0 CG A:ASP269 3.0 20.8 1.0 H30 A:KRU605 3.0 20.8 1.0 OD1 A:ASP181 3.0 18.7 1.0 C2 A:KRU605 3.0 19.7 1.0 C6 A:KRU605 3.0 20.9 1.0 C3 A:KRU605 3.1 20.7 1.0 CG A:HIS183 3.1 20.9 1.0 OD1 A:ASP269 3.3 19.8 1.0 H29 A:KRU605 3.3 21.0 1.0 H23 A:KRU605 3.6 20.7 1.0 CB A:HIS183 3.6 20.2 1.0 N A:HIS183 3.9 19.1 1.0 NE2 A:HIS145 4.1 19.8 1.0 NE2 A:HIS183 4.1 21.9 1.0 N14 A:KRU605 4.2 20.6 1.0 CA A:GLY306 4.2 19.6 1.0 CG2 A:ILE182 4.2 19.4 1.0 CD2 A:HIS183 4.2 21.6 1.0 C4 A:KRU605 4.2 21.3 1.0 CB A:ASP181 4.3 17.9 1.0 CB A:ASP269 4.3 19.8 1.0 C5 A:KRU605 4.3 21.1 1.0 N A:GLY306 4.4 20.1 1.0 CA A:HIS183 4.4 20.6 1.0 N A:ILE182 4.5 19.9 1.0 H28 A:KRU605 4.5 21.3 1.0 CE1 A:HIS145 4.5 19.1 1.0 H42 A:KRU605 4.6 23.1 1.0 H24 A:KRU605 4.7 21.1 1.0 OH A:TYR308 4.7 24.8 1.0 NE2 A:HIS146 4.9 21.5 1.0 C22 A:KRU605 4.9 23.2 1.0 CE1 A:TYR308 4.9 23.8 1.0 C A:ILE182 4.9 19.6 1.0 CA A:ASP181 5.0 18.8 1.0

Zinc binding site 2 out of 3 in the Inhibitor 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 Inhibitor Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:19.2 occ:1.00 H25 B:KRU609 1.3 20.1 1.0 OD2 B:ASP269 1.9 19.3 1.0 ND1 B:HIS183 2.0 18.2 1.0 OD2 B:ASP181 2.0 17.4 1.0 N7 B:KRU609 2.1 20.1 1.0 H26 B:KRU609 2.5 20.0 1.0 O1 B:KRU609 2.5 19.3 1.0 CG B:ASP181 2.8 17.9 1.0 CE1 B:HIS183 2.9 19.4 1.0 CG B:ASP269 2.9 19.9 1.0 C2 B:KRU609 3.0 18.9 1.0 OD1 B:ASP181 3.0 16.2 1.0 C3 B:KRU609 3.0 19.4 1.0 H30 B:KRU609 3.0 18.4 1.0 C6 B:KRU609 3.1 18.4 1.0 CG B:HIS183 3.1 19.5 1.0 OD1 B:ASP269 3.3 17.7 1.0 H29 B:KRU609 3.4 18.5 1.0 H23 B:KRU609 3.5 19.4 1.0 CB B:HIS183 3.6 16.7 1.0 N B:HIS183 3.9 16.9 1.0 NE2 B:HIS145 4.1 19.2 1.0 NE2 B:HIS183 4.1 19.6 1.0 N14 B:KRU609 4.1 21.0 1.0 CA B:GLY306 4.2 16.9 1.0 C4 B:KRU609 4.2 20.9 1.0 CD2 B:HIS183 4.2 20.4 1.0 CG2 B:ILE182 4.2 17.7 1.0 CB B:ASP181 4.3 15.8 1.0 CB B:ASP269 4.3 17.4 1.0 C5 B:KRU609 4.3 19.2 1.0 CA B:HIS183 4.4 17.6 1.0 N B:GLY306 4.4 16.7 1.0 H28 B:KRU609 4.4 20.8 1.0 CE1 B:HIS145 4.5 17.8 1.0 N B:ILE182 4.5 16.8 1.0 H36 B:KRU609 4.7 21.7 1.0 H24 B:KRU609 4.7 19.2 1.0 OH B:TYR308 4.7 21.3 1.0 CE1 B:TYR308 4.9 18.7 1.0 NE2 B:HIS146 4.9 20.8 1.0 C15 B:KRU609 4.9 21.8 1.0 C B:ILE182 4.9 17.9 1.0 CA B:ASP181 5.0 16.4 1.0

Zinc binding site 3 out of 3 in the Inhibitor 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 Inhibitor Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:27.7 occ:1.00 H25 C:KRU606 1.3 15.5 0.6 OD2 C:ASP269 2.0 27.8 1.0 ND1 C:HIS183 2.0 27.2 1.0 OD2 C:ASP181 2.0 26.2 1.0 N7 C:KRU606 2.1 15.4 0.6 O1 C:KRU606 2.5 16.8 0.6 H26 C:KRU606 2.5 15.4 0.6 CG C:ASP181 2.8 27.2 1.0 CE1 C:HIS183 2.9 25.1 1.0 H30 C:KRU606 2.9 15.9 0.6 CG C:ASP269 2.9 29.7 1.0 OD1 C:ASP181 3.0 26.8 1.0 C2 C:KRU606 3.0 17.3 0.6 C6 C:KRU606 3.0 15.9 0.6 C3 C:KRU606 3.1 16.7 0.6 CG C:HIS183 3.1 27.2 1.0 H29 C:KRU606 3.3 15.9 0.6 OD1 C:ASP269 3.3 27.6 1.0 H23 C:KRU606 3.6 16.7 0.6 CB C:HIS183 3.6 25.7 1.0 N C:HIS183 3.9 26.8 1.0 NE2 C:HIS145 4.1 26.6 1.0 NE2 C:HIS183 4.1 28.8 1.0 N14 C:KRU606 4.1 19.7 0.6 CG2 C:ILE182 4.2 29.3 1.0 CA C:GLY306 4.2 27.7 1.0 C4 C:KRU606 4.2 16.2 0.6 CD2 C:HIS183 4.2 28.6 1.0 CB C:ASP181 4.2 24.8 1.0 CB C:ASP269 4.3 27.7 1.0 C5 C:KRU606 4.3 16.7 0.6 CA C:HIS183 4.4 25.0 1.0 H28 C:KRU606 4.4 16.1 0.6 N C:GLY306 4.4 27.8 1.0 N C:ILE182 4.5 26.8 1.0 CE1 C:HIS145 4.5 26.8 1.0 H36 C:KRU606 4.6 21.5 0.6 H24 C:KRU606 4.7 16.6 0.6 OH C:TYR308 4.7 35.9 1.0 C C:ILE182 4.9 27.2 1.0 C15 C:KRU606 4.9 21.5 0.6 NE2 C:HIS146 4.9 26.9 1.0 CE1 C:TYR308 4.9 31.9 1.0 C C:ASP181 5.0 26.8 1.0 H43 C:KRU606 5.0 18.9 0.6 CA C:ASP181 5.0 25.3 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