Zinc in PDB 6xdm: Structure of Human HDAC2 in Complex with An Aryl Ketone Inhibitor

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

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

Resolution Low / High (Å)	22.76 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.255, 99.495, 139.850, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 18.9

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

Fluorine	(F)	3 atoms
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with An Aryl Ketone Inhibitor (pdb code 6xdm). 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 Aryl Ketone Inhibitor, PDB code: 6xdm:
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 Aryl 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 Aryl Ketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.4 occ:1.00 OD2 A:ASP265 1.9 13.4 1.0 OD1 A:ASP177 2.0 12.2 1.0 ND1 A:HIS179 2.0 13.3 1.0 O1 A:V1D411 2.1 15.4 1.0 O2 A:V1D411 2.5 15.2 1.0 C11 A:V1D411 2.8 16.2 1.0 CG A:ASP177 2.8 12.5 1.0 CG A:ASP265 2.9 12.8 1.0 CE1 A:HIS179 2.9 14.4 1.0 OD2 A:ASP177 3.0 12.4 1.0 CG A:HIS179 3.2 12.6 1.0 OD1 A:ASP265 3.2 12.3 1.0 CB A:HIS179 3.6 12.1 1.0 N A:HIS179 3.9 11.4 1.0 C12 A:V1D411 3.9 17.0 1.0 C10 A:V1D411 3.9 16.1 1.0 C9 A:V1D411 4.0 16.2 1.0 CA A:GLY302 4.1 12.5 1.0 NE2 A:HIS179 4.1 15.0 1.0 CG2 A:ILE178 4.1 12.6 1.0 CB A:ASP177 4.2 11.4 1.0 CD2 A:HIS179 4.2 13.4 1.0 CB A:ASP265 4.3 12.8 1.0 N A:ILE178 4.3 9.9 1.0 CA A:HIS179 4.4 11.6 1.0 OH A:TYR304 4.4 14.2 1.0 N A:GLY302 4.4 12.8 1.0 CE2 A:TYR304 4.4 12.4 1.0 NE2 A:HIS141 4.5 15.0 1.0 N2 A:V1D411 4.5 17.2 1.0 C A:ILE178 4.8 11.9 1.0 CE1 A:HIS141 4.9 15.1 1.0 C A:ASP177 4.9 10.9 1.0 NE2 A:HIS142 4.9 14.9 1.0 CA A:ASP177 4.9 10.1 1.0 CZ A:TYR304 4.9 13.5 1.0 C13 A:V1D411 4.9 17.2 1.0 CA A:ILE178 5.0 10.2 1.0

Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.8 occ:1.00 OD2 B:ASP265 2.0 13.9 1.0 OD1 B:ASP177 2.0 11.5 1.0 ND1 B:HIS179 2.0 11.8 1.0 O1 B:V1D408 2.0 14.0 1.0 O2 B:V1D408 2.5 12.6 1.0 C11 B:V1D408 2.8 14.1 1.0 CG B:ASP177 2.8 11.5 1.0 CE1 B:HIS179 2.9 12.6 1.0 CG B:ASP265 2.9 12.4 1.0 OD2 B:ASP177 3.0 11.5 1.0 CG B:HIS179 3.1 11.1 1.0 OD1 B:ASP265 3.2 10.8 1.0 CB B:HIS179 3.6 10.9 1.0 N B:HIS179 3.8 9.7 1.0 C12 B:V1D408 3.9 15.7 1.0 C10 B:V1D408 3.9 14.4 1.0 C9 B:V1D408 4.0 14.1 1.0 CA B:GLY302 4.1 11.2 1.0 NE2 B:HIS179 4.1 13.0 1.0 CG2 B:ILE178 4.2 11.8 1.0 CB B:ASP177 4.2 9.1 1.0 CD2 B:HIS179 4.2 12.0 1.0 CB B:ASP265 4.3 10.8 1.0 N B:ILE178 4.3 9.1 1.0 CA B:HIS179 4.4 9.8 1.0 OH B:TYR304 4.4 13.4 1.0 N2 B:V1D408 4.4 16.6 1.0 NE2 B:HIS141 4.4 12.7 1.0 CE2 B:TYR304 4.5 10.4 1.0 N B:GLY302 4.5 10.5 1.0 C B:ILE178 4.8 10.3 1.0 CE1 B:HIS141 4.9 13.9 1.0 C13 B:V1D408 4.9 16.3 1.0 NE2 B:HIS142 4.9 12.3 1.0 C B:ASP177 4.9 9.2 1.0 CA B:ASP177 4.9 8.8 1.0 CZ B:TYR304 4.9 11.7 1.0 CA B:ILE178 5.0 9.9 1.0

Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:16.7 occ:1.00 OD2 C:ASP265 1.9 15.3 1.0 ND1 C:HIS179 2.0 16.9 1.0 OD1 C:ASP177 2.0 15.2 1.0 O1 C:V1D410 2.1 17.2 1.0 O2 C:V1D410 2.4 17.0 1.0 C11 C:V1D410 2.8 18.1 1.0 CG C:ASP177 2.8 15.8 1.0 CG C:ASP265 2.9 16.1 1.0 CE1 C:HIS179 2.9 17.0 1.0 OD2 C:ASP177 3.0 17.5 1.0 CG C:HIS179 3.1 15.1 1.0 OD1 C:ASP265 3.2 16.3 1.0 CB C:HIS179 3.5 14.1 1.0 N C:HIS179 3.8 14.0 1.0 C10 C:V1D410 3.9 18.7 1.0 C12 C:V1D410 3.9 19.1 1.0 C9 C:V1D410 4.0 19.0 1.0 CA C:GLY302 4.1 17.6 1.0 NE2 C:HIS179 4.1 17.0 1.0 CG2 C:ILE178 4.1 15.1 1.0 CD2 C:HIS179 4.2 15.9 1.0 CB C:ASP177 4.3 15.7 1.0 CB C:ASP265 4.3 14.8 1.0 N C:ILE178 4.3 14.7 1.0 CA C:HIS179 4.3 13.6 1.0 OH C:TYR304 4.4 19.3 1.0 N C:GLY302 4.4 16.5 1.0 N2 C:V1D410 4.4 19.8 1.0 CE2 C:TYR304 4.5 18.4 1.0 NE2 C:HIS141 4.5 17.6 1.0 C C:ILE178 4.8 14.8 1.0 NE2 C:HIS142 4.9 16.3 1.0 CZ C:TYR304 4.9 19.4 1.0 C C:ASP177 4.9 15.5 1.0 CA C:ILE178 4.9 14.6 1.0 CE1 C:HIS141 4.9 17.8 1.0 C13 C:V1D410 4.9 19.8 1.0 CA C:ASP177 5.0 15.6 1.0

J.Liu, J.Kelly, W.Yu, D.Clausen, Y.Yu, H.Kim, J.L.Duffy, C.C.Chung, R.W.Myers, S.Carroll, D.J.Klein, J.Fells, M.K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.A.Kozlowski. Selective Class I Hdac Inhibitors Based on Aryl Ketone Zinc Binding Induce Hiv-1 Protein For Clearance. Acs Med.Chem.Lett. V. 11 1476 2020.
ISSN: ISSN 1948-5875
PubMed: 32676157
DOI: 10.1021/ACSMEDCHEMLETT.0C00302