Zinc in PDB 6xeb: Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)

All present enzymatic activity of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E):
3.5.1.98;

The structure of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E), PDB code: 6xeb was solved by D.J.Klein, D.Clausen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.93 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.390, 99.030, 139.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.3

The structure of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E) 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 Ketone Inhibitor (Compound E) (pdb code 6xeb). 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 Ketone Inhibitor (Compound E), PDB code: 6xeb:
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 Ketone Inhibitor (Compound E)


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 Ketone Inhibitor (Compound E) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.3 occ:1.00 OD2 A:ASP265 1.9 12.9 1.0 OD1 A:ASP177 2.0 14.0 1.0 ND1 A:HIS179 2.0 14.3 1.0 O3 A:V1P411 2.1 15.4 1.0 O2 A:V1P411 2.5 15.5 1.0 C21 A:V1P411 2.8 16.2 1.0 CG A:ASP177 2.8 13.8 1.0 CG A:ASP265 2.9 13.0 1.0 CE1 A:HIS179 2.9 14.6 1.0 OD2 A:ASP177 3.0 13.4 1.0 CG A:HIS179 3.2 14.2 1.0 OD1 A:ASP265 3.2 13.0 1.0 CB A:HIS179 3.6 14.0 1.0 C22 A:V1P411 3.8 17.9 1.0 N A:HIS179 3.9 12.7 1.0 C20 A:V1P411 3.9 15.4 1.0 C19 A:V1P411 4.0 15.8 1.0 CA A:GLY302 4.1 13.4 1.0 NE2 A:HIS179 4.1 14.9 1.0 CG2 A:ILE178 4.1 13.0 1.0 CB A:ASP177 4.2 13.0 1.0 CB A:ASP265 4.2 13.3 1.0 CD2 A:HIS179 4.2 14.2 1.0 OH A:TYR304 4.3 13.9 1.0 N A:ILE178 4.3 11.2 1.0 NE2 A:HIS141 4.4 15.0 1.0 CA A:HIS179 4.4 13.2 1.0 N A:GLY302 4.4 13.0 1.0 CE2 A:TYR304 4.4 13.7 1.0 CE1 A:HIS141 4.8 15.4 1.0 C23 A:V1P411 4.8 18.3 1.0 C A:ILE178 4.8 13.4 1.0 CZ A:TYR304 4.9 13.5 1.0 C A:ASP177 4.9 12.2 1.0 CA A:ASP177 4.9 11.7 1.0 NE2 A:HIS142 4.9 15.2 1.0 CA A:ILE178 5.0 12.1 1.0

Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


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 Ketone Inhibitor (Compound E) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.9 occ:1.00 OD2 B:ASP265 2.0 13.3 1.0 OD1 B:ASP177 2.0 12.5 1.0 ND1 B:HIS179 2.0 12.8 1.0 O2 B:V1P408 2.1 14.5 1.0 O3 B:V1P408 2.5 12.3 1.0 C21 B:V1P408 2.7 14.1 1.0 CG B:ASP177 2.8 13.1 1.0 CE1 B:HIS179 2.9 14.0 1.0 CG B:ASP265 2.9 12.7 1.0 OD2 B:ASP177 3.0 12.2 1.0 CG B:HIS179 3.1 12.3 1.0 OD1 B:ASP265 3.3 12.3 1.0 CB B:HIS179 3.6 11.6 1.0 C22 B:V1P408 3.8 15.8 1.0 C20 B:V1P408 3.9 14.1 1.0 N B:HIS179 3.9 11.9 1.0 C19 B:V1P408 3.9 14.2 1.0 CA B:GLY302 4.0 12.7 1.0 NE2 B:HIS179 4.1 14.2 1.0 CG2 B:ILE178 4.2 12.4 1.0 CD2 B:HIS179 4.2 13.1 1.0 CB B:ASP177 4.2 11.8 1.0 CB B:ASP265 4.3 11.1 1.0 OH B:TYR304 4.3 13.8 1.0 N B:ILE178 4.4 10.9 1.0 CA B:HIS179 4.4 11.5 1.0 NE2 B:HIS141 4.4 13.6 1.0 CE2 B:TYR304 4.4 11.0 1.0 N B:GLY302 4.4 11.9 1.0 CE1 B:HIS141 4.8 14.5 1.0 C23 B:V1P408 4.8 16.2 1.0 C B:ILE178 4.8 12.1 1.0 CZ B:TYR304 4.9 12.3 1.0 C B:ASP177 4.9 11.6 1.0 CA B:ASP177 4.9 11.5 1.0 NE2 B:HIS142 5.0 14.0 1.0

Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


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 Ketone Inhibitor (Compound E) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:17.4 occ:1.00 OD1 C:ASP177 1.9 13.8 1.0 OD2 C:ASP265 2.0 17.5 1.0 ND1 C:HIS179 2.0 18.0 1.0 O2 C:V1P410 2.1 18.2 1.0 O3 C:V1P410 2.4 17.7 1.0 C21 C:V1P410 2.8 18.7 1.0 CG C:ASP177 2.8 15.0 1.0 CG C:ASP265 3.0 16.9 1.0 CE1 C:HIS179 3.0 17.5 1.0 OD2 C:ASP177 3.0 16.8 1.0 CG C:HIS179 3.1 16.0 1.0 OD1 C:ASP265 3.3 17.3 1.0 CB C:HIS179 3.5 15.7 1.0 C22 C:V1P410 3.8 18.6 1.0 N C:HIS179 3.9 15.2 1.0 C20 C:V1P410 3.9 18.9 1.0 C19 C:V1P410 3.9 19.1 1.0 CA C:GLY302 4.1 17.8 1.0 NE2 C:HIS179 4.1 16.8 1.0 CG2 C:ILE178 4.2 16.4 1.0 CB C:ASP177 4.2 16.0 1.0 CD2 C:HIS179 4.2 16.1 1.0 OH C:TYR304 4.3 19.8 1.0 CB C:ASP265 4.3 16.4 1.0 CA C:HIS179 4.4 15.4 1.0 N C:ILE178 4.4 15.4 1.0 NE2 C:HIS141 4.4 16.8 1.0 CE2 C:TYR304 4.4 20.0 1.0 N C:GLY302 4.4 17.0 1.0 CE1 C:HIS141 4.8 17.6 1.0 C23 C:V1P410 4.8 18.6 1.0 C C:ILE178 4.8 15.6 1.0 CZ C:TYR304 4.9 20.4 1.0 C C:ASP177 4.9 16.1 1.0 NE2 C:HIS142 4.9 17.9 1.0 CA C:ASP177 5.0 15.8 1.0 CA C:ILE178 5.0 15.4 1.0

D.J.Clausen, J.Liu, W.Yu, J.L.Duffy, C.C.Chung, R.W.Myers, D.J.Klein, J.Fells, K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Development of A Selective Hdac Inhibitor Aimed at Reactivating the Hiv Latent Reservoir. Bioorg.Med.Chem.Lett. V. 30 27367 2020.
ISSN: ESSN 1464-3405
PubMed: 32738976
DOI: 10.1016/J.BMCL.2020.127367