Zinc in PDB 6wbw: Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor:
3.5.1.98;

The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor, PDB code: 6wbw was solved by D.J.Klein, W.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.33 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.970, 98.280, 139.050, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.7

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

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor (pdb code 6wbw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor, PDB code: 6wbw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.8 occ:1.00 OD2 A:ASP265 1.9 15.9 1.0 OD1 A:ASP177 2.0 15.4 1.0 ND1 A:HIS179 2.1 16.0 1.0 O35 A:TV1401 2.1 15.4 1.0 O34 A:TV1401 2.5 15.6 1.0 C27 A:TV1401 2.8 16.7 1.0 CG A:ASP177 2.8 15.9 1.0 CG A:ASP265 2.9 13.0 1.0 CE1 A:HIS179 2.9 17.0 1.0 OD2 A:ASP177 3.0 15.7 1.0 CG A:HIS179 3.2 16.4 1.0 OD1 A:ASP265 3.2 14.3 1.0 CB A:HIS179 3.6 15.4 1.0 C20 A:TV1401 3.8 19.6 1.0 N A:HIS179 3.9 13.6 1.0 C25 A:TV1401 3.9 15.2 1.0 C23 A:TV1401 4.0 17.1 1.0 CA A:GLY302 4.0 14.4 1.0 NE2 A:HIS179 4.1 17.6 1.0 CG2 A:ILE178 4.1 15.0 1.0 CB A:ASP177 4.2 13.6 1.0 CD2 A:HIS179 4.2 17.6 1.0 CB A:ASP265 4.3 15.1 1.0 OH A:TYR304 4.3 16.1 1.0 N A:GLY302 4.3 14.6 1.0 CA A:HIS179 4.3 14.2 1.0 CE2 A:TYR304 4.3 14.9 1.0 N A:ILE178 4.4 14.0 1.0 NE2 A:HIS141 4.4 16.0 1.0 CZ A:TYR304 4.8 16.1 1.0 CE1 A:HIS141 4.8 15.3 1.0 C17 A:TV1401 4.8 19.6 1.0 C A:ILE178 4.9 16.1 1.0 C A:ASP177 4.9 14.9 1.0 CA A:ASP177 4.9 12.9 1.0 NE2 A:HIS142 4.9 16.3 1.0

Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:14.4 occ:1.00 OD2 B:ASP265 2.0 15.1 1.0 OD1 B:ASP177 2.0 14.3 1.0 ND1 B:HIS179 2.0 14.8 1.0 O35 B:TV1401 2.1 14.9 1.0 O34 B:TV1401 2.5 13.1 1.0 C27 B:TV1401 2.8 15.5 1.0 CG B:ASP177 2.8 14.5 1.0 CE1 B:HIS179 2.9 15.6 1.0 CG B:ASP265 2.9 14.3 1.0 OD2 B:ASP177 3.0 13.7 1.0 CG B:HIS179 3.1 14.5 1.0 OD1 B:ASP265 3.2 14.2 1.0 CB B:HIS179 3.6 12.8 1.0 C20 B:TV1401 3.8 15.8 1.0 C25 B:TV1401 3.9 16.6 1.0 N B:HIS179 3.9 12.7 1.0 C23 B:TV1401 3.9 15.8 1.0 CA B:GLY302 4.0 13.0 1.0 NE2 B:HIS179 4.1 15.8 1.0 CG2 B:ILE178 4.2 14.7 1.0 CD2 B:HIS179 4.2 16.3 1.0 CB B:ASP177 4.2 12.9 1.0 CB B:ASP265 4.3 12.6 1.0 OH B:TYR304 4.3 14.1 1.0 NE2 B:HIS141 4.3 14.2 1.0 CE2 B:TYR304 4.3 11.9 1.0 CA B:HIS179 4.4 12.3 1.0 N B:GLY302 4.4 12.2 1.0 N B:ILE178 4.4 11.7 1.0 CE1 B:HIS141 4.7 14.7 1.0 CZ B:TYR304 4.8 13.3 1.0 C17 B:TV1401 4.8 16.9 1.0 C B:ILE178 4.9 14.7 1.0 C B:ASP177 4.9 13.8 1.0 CA B:ASP177 4.9 12.5 1.0 NE2 B:HIS142 4.9 15.9 1.0

Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:19.0 occ:1.00 OD2 C:ASP265 2.0 19.6 1.0 OD1 C:ASP177 2.0 17.8 1.0 O35 C:TV1401 2.1 18.5 1.0 ND1 C:HIS179 2.1 20.9 1.0 O34 C:TV1401 2.3 18.2 1.0 C27 C:TV1401 2.7 20.9 1.0 CG C:ASP177 2.8 17.7 1.0 CG C:ASP265 3.0 20.2 1.0 OD2 C:ASP177 3.0 20.2 1.0 CE1 C:HIS179 3.0 18.9 1.0 CG C:HIS179 3.2 19.1 1.0 OD1 C:ASP265 3.3 19.8 1.0 CB C:HIS179 3.5 17.4 1.0 C20 C:TV1401 3.8 21.5 1.0 C25 C:TV1401 3.8 19.8 1.0 N C:HIS179 3.9 17.0 1.0 C23 C:TV1401 3.9 19.3 1.0 CA C:GLY302 4.0 18.3 1.0 CG2 C:ILE178 4.2 20.4 1.0 NE2 C:HIS179 4.2 18.8 1.0 CB C:ASP177 4.3 17.1 1.0 OH C:TYR304 4.3 20.9 1.0 CD2 C:HIS179 4.3 19.4 1.0 CB C:ASP265 4.3 18.9 1.0 NE2 C:HIS141 4.3 17.7 1.0 CA C:HIS179 4.4 16.5 1.0 N C:GLY302 4.4 18.9 1.0 N C:ILE178 4.4 17.0 1.0 CE2 C:TYR304 4.4 22.0 1.0 CE1 C:HIS141 4.8 18.3 1.0 C C:ILE178 4.8 18.9 1.0 CZ C:TYR304 4.8 23.9 1.0 C17 C:TV1401 4.8 21.9 1.0 NE2 C:HIS142 4.9 18.4 1.0 C C:ASP177 4.9 18.3 1.0 CA C:ASP177 4.9 16.2 1.0 CA C:ILE178 5.0 16.8 1.0

W.Yu, J.Liu, Y.Yu, V.Zhang, D.Clausen, J.Kelly, S.Wolkenberg, D.Beshore, J.L.Duffy, C.C.Chang, R.W.Myers, D.J.Klein, J.Fells, K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Discovery of Ethyl Ketone-Based Hdacs 1, 2, and 3 Selective Inhibitors For Hiv Latency Reactivation. Bioorg.Med.Chem.Lett. 27197 2020.
ISSN: ESSN 1464-3405
PubMed: 32331932
DOI: 10.1016/J.BMCL.2020.127197