Zinc in PDB 7mot: Structure of HDAC2 in Complex with An Inhibitor (Compound 9)

All present enzymatic activity of Structure of HDAC2 in Complex with An Inhibitor (Compound 9):
3.5.1.98;

The structure of Structure of HDAC2 in Complex with An Inhibitor (Compound 9), PDB code: 7mot 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)	22.52 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.417, 99.064, 139.622, 90, 90, 90
R / Rfree (%)	17.8 / 20.3

The structure of Structure of HDAC2 in Complex with An Inhibitor (Compound 9) also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9) (pdb code 7mot). 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 HDAC2 in Complex with An Inhibitor (Compound 9), PDB code: 7mot:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of HDAC2 in Complex with An Inhibitor (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.4 occ:1.00 OD2 A:ASP265 1.9 11.9 1.0 OD1 A:ASP177 2.0 12.6 1.0 ND1 A:HIS179 2.0 13.6 1.0 O3 A:V1P411 2.1 14.5 1.0 O2 A:V1P411 2.5 14.4 1.0 C21 A:V1P411 2.8 15.2 1.0 CG A:ASP177 2.8 12.7 1.0 CG A:ASP265 2.9 12.2 1.0 CE1 A:HIS179 2.9 14.1 1.0 OD2 A:ASP177 3.0 12.7 1.0 CG A:HIS179 3.2 13.5 1.0 OD1 A:ASP265 3.2 12.2 1.0 CB A:HIS179 3.6 13.2 1.0 C22 A:V1P411 3.8 17.3 1.0 N A:HIS179 3.9 11.8 1.0 C20 A:V1P411 3.9 14.6 1.0 C19 A:V1P411 4.0 15.1 1.0 CA A:GLY302 4.1 12.4 1.0 NE2 A:HIS179 4.1 14.5 1.0 CG2 A:ILE178 4.2 11.5 1.0 CB A:ASP177 4.2 12.2 1.0 CB A:ASP265 4.2 12.6 1.0 CD2 A:HIS179 4.2 13.9 1.0 N A:ILE178 4.3 10.0 1.0 OH A:TYR304 4.3 13.1 1.0 NE2 A:HIS141 4.4 13.8 1.0 CA A:HIS179 4.4 12.2 1.0 N A:GLY302 4.4 12.1 1.0 CE2 A:TYR304 4.4 12.9 1.0 CE1 A:HIS141 4.8 14.3 1.0 C23 A:V1P411 4.8 17.6 1.0 C A:ILE178 4.8 12.2 1.0 CZ A:TYR304 4.9 12.8 1.0 C A:ASP177 4.9 11.0 1.0 CA A:ASP177 4.9 10.7 1.0 NE2 A:HIS142 4.9 14.2 1.0 CA A:ILE178 5.0 10.7 1.0

Zinc binding site 2 out of 3 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of HDAC2 in Complex with An Inhibitor (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.9 occ:1.00 OD2 B:ASP265 2.0 12.4 1.0 OD1 B:ASP177 2.0 11.4 1.0 ND1 B:HIS179 2.0 11.3 1.0 O2 B:V1P408 2.0 13.4 1.0 O3 B:V1P408 2.5 11.2 1.0 C21 B:V1P408 2.7 12.9 1.0 CG B:ASP177 2.8 12.4 1.0 CE1 B:HIS179 2.9 12.6 1.0 CG B:ASP265 2.9 11.7 1.0 OD2 B:ASP177 3.0 11.5 1.0 CG B:HIS179 3.1 11.0 1.0 OD1 B:ASP265 3.3 11.0 1.0 CB B:HIS179 3.6 10.6 1.0 C22 B:V1P408 3.8 14.8 1.0 C20 B:V1P408 3.9 12.6 1.0 N B:HIS179 3.9 10.3 1.0 C19 B:V1P408 3.9 12.5 1.0 CA B:GLY302 4.1 11.4 1.0 NE2 B:HIS179 4.1 12.7 1.0 CG2 B:ILE178 4.2 11.6 1.0 CD2 B:HIS179 4.2 11.6 1.0 CB B:ASP177 4.2 11.2 1.0 CB B:ASP265 4.3 10.9 1.0 OH B:TYR304 4.3 12.8 1.0 CA B:HIS179 4.4 10.3 1.0 NE2 B:HIS141 4.4 12.4 1.0 N B:ILE178 4.4 9.6 1.0 CE2 B:TYR304 4.4 10.0 1.0 N B:GLY302 4.4 10.8 1.0 CE1 B:HIS141 4.8 13.4 1.0 C23 B:V1P408 4.8 15.2 1.0 C B:ILE178 4.8 10.6 1.0 CZ B:TYR304 4.9 11.7 1.0 C B:ASP177 4.9 10.8 1.0 CA B:ASP177 4.9 10.8 1.0 NE2 B:HIS142 5.0 13.2 1.0

Zinc binding site 3 out of 3 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of HDAC2 in Complex with An Inhibitor (Compound 9) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:16.6 occ:1.00 OD1 C:ASP177 1.9 13.0 1.0 OD2 C:ASP265 2.0 16.0 1.0 ND1 C:HIS179 2.0 16.9 1.0 O2 C:V1P410 2.1 17.2 1.0 O3 C:V1P410 2.4 16.8 1.0 C21 C:V1P410 2.8 17.6 1.0 CG C:ASP177 2.8 14.2 1.0 CE1 C:HIS179 2.9 16.5 1.0 CG C:ASP265 2.9 15.6 1.0 OD2 C:ASP177 3.0 15.7 1.0 CG C:HIS179 3.1 14.6 1.0 OD1 C:ASP265 3.3 15.8 1.0 CB C:HIS179 3.6 14.4 1.0 C22 C:V1P410 3.8 17.8 1.0 N C:HIS179 3.9 14.1 1.0 C20 C:V1P410 3.9 17.8 1.0 C19 C:V1P410 4.0 17.9 1.0 CA C:GLY302 4.1 16.8 1.0 NE2 C:HIS179 4.1 15.6 1.0 CG2 C:ILE178 4.2 15.7 1.0 CB C:ASP177 4.2 15.2 1.0 CD2 C:HIS179 4.2 14.7 1.0 CB C:ASP265 4.3 15.8 1.0 OH C:TYR304 4.3 18.3 1.0 N C:ILE178 4.4 14.5 1.0 CA C:HIS179 4.4 14.4 1.0 NE2 C:HIS141 4.4 16.2 1.0 CE2 C:TYR304 4.4 19.1 1.0 N C:GLY302 4.4 15.9 1.0 CE1 C:HIS141 4.8 16.7 1.0 C23 C:V1P410 4.8 17.9 1.0 C C:ILE178 4.8 14.6 1.0 CZ C:TYR304 4.9 19.3 1.0 C C:ASP177 4.9 15.3 1.0 NE2 C:HIS142 4.9 16.7 1.0 CA C:ASP177 5.0 14.8 1.0 CA C:ILE178 5.0 14.5 1.0

W.Yu, J.Fells, D.Clausen, J.Liu, D.J.Klein, C.Christine Chung, R.W.Myers, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Discovery of Macrocyclic Hdacs 1, 2, and 3 Selective Inhibitors For Hiv Latency Reactivation. Bioorg.Med.Chem.Lett. V. 47 28168 2021.
ISSN: ESSN 1464-3405
PubMed: 34091041
DOI: 10.1016/J.BMCL.2021.128168