Zinc in PDB 7moz: Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)

All present enzymatic activity of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25):
3.5.1.98;

The structure of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25), PDB code: 7moz 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)	22.55 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.478, 98.989, 139.489, 90, 90, 90
R / Rfree (%)	17.6 / 20.1

The structure of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) (pdb code 7moz). 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 A Macrocyclic Inhibitor (Compound 25), PDB code: 7moz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)


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 A Macrocyclic Inhibitor (Compound 25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.3 occ:1.00 OD2 A:ASP265 1.9 13.3 1.0 OD1 A:ASP177 2.0 13.1 1.0 O1 A:ZL4411 2.0 13.8 1.0 ND1 A:HIS179 2.0 14.1 1.0 O A:ZL4411 2.5 13.9 1.0 C2 A:ZL4411 2.8 15.1 1.0 CG A:ASP177 2.8 13.1 1.0 CG A:ASP265 2.9 12.6 1.0 CE1 A:HIS179 2.9 14.5 1.0 OD2 A:ASP177 3.0 12.7 1.0 CG A:HIS179 3.2 13.4 1.0 OD1 A:ASP265 3.2 12.2 1.0 CB A:HIS179 3.6 13.1 1.0 C1 A:ZL4411 3.8 16.6 1.0 C3 A:ZL4411 3.8 15.6 1.0 N A:HIS179 3.9 11.3 1.0 C4 A:ZL4411 3.9 15.7 1.0 CA A:GLY302 4.0 13.0 1.0 NE2 A:HIS179 4.1 14.6 1.0 CG2 A:ILE178 4.2 12.0 1.0 CB A:ASP177 4.2 11.7 1.0 CD2 A:HIS179 4.2 13.8 1.0 CB A:ASP265 4.2 13.5 1.0 OH A:TYR304 4.3 13.4 1.0 N A:ILE178 4.3 10.7 1.0 CE2 A:TYR304 4.4 12.8 1.0 CA A:HIS179 4.4 12.3 1.0 NE2 A:HIS141 4.4 14.2 1.0 N A:GLY302 4.4 12.3 1.0 C A:ZL4411 4.8 17.4 1.0 CZ A:TYR304 4.8 13.1 1.0 C A:ILE178 4.8 12.2 1.0 CE1 A:HIS141 4.9 14.2 1.0 NE2 A:HIS142 4.9 14.6 1.0 C A:ASP177 4.9 11.8 1.0 CA A:ASP177 4.9 10.8 1.0 CA A:ILE178 5.0 11.3 1.0

Zinc binding site 2 out of 3 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)


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 A Macrocyclic Inhibitor (Compound 25) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.4 occ:1.00 OD2 B:ASP265 1.9 13.2 1.0 OD1 B:ASP177 2.0 11.3 1.0 O1 B:ZL4408 2.0 13.1 1.0 ND1 B:HIS179 2.0 12.3 1.0 O B:ZL4408 2.5 12.1 1.0 C2 B:ZL4408 2.7 13.6 1.0 CG B:ASP177 2.8 11.7 1.0 CE1 B:HIS179 2.9 13.1 1.0 CG B:ASP265 2.9 12.5 1.0 OD2 B:ASP177 3.0 11.8 1.0 CG B:HIS179 3.2 11.8 1.0 OD1 B:ASP265 3.3 11.3 1.0 CB B:HIS179 3.6 11.1 1.0 C1 B:ZL4408 3.8 15.4 1.0 N B:HIS179 3.8 10.8 1.0 C3 B:ZL4408 3.8 14.2 1.0 C4 B:ZL4408 3.9 14.7 1.0 CA B:GLY302 4.0 11.7 1.0 NE2 B:HIS179 4.1 13.3 1.0 CG2 B:ILE178 4.2 11.8 1.0 CD2 B:HIS179 4.2 13.2 1.0 CB B:ASP177 4.2 10.5 1.0 CB B:ASP265 4.3 11.6 1.0 OH B:TYR304 4.3 12.9 1.0 CA B:HIS179 4.3 10.5 1.0 NE2 B:HIS141 4.4 13.6 1.0 N B:ILE178 4.4 9.6 1.0 CE2 B:TYR304 4.4 10.8 1.0 N B:GLY302 4.4 10.7 1.0 C B:ILE178 4.8 11.2 1.0 CE1 B:HIS141 4.8 13.8 1.0 C B:ZL4408 4.8 16.1 1.0 CZ B:TYR304 4.8 11.8 1.0 C B:ASP177 4.9 10.7 1.0 CA B:ASP177 4.9 10.4 1.0 NE2 B:HIS142 4.9 14.9 1.0 CA B:ILE178 5.0 10.1 1.0

Zinc binding site 3 out of 3 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)


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 A Macrocyclic Inhibitor (Compound 25) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:15.6 occ:1.00 OD1 C:ASP177 2.0 13.2 1.0 OD2 C:ASP265 2.0 15.2 1.0 ND1 C:HIS179 2.0 16.8 1.0 O1 C:ZL4410 2.1 16.1 1.0 O C:ZL4410 2.5 15.7 1.0 C2 C:ZL4410 2.8 16.4 1.0 CG C:ASP177 2.8 14.3 1.0 CG C:ASP265 2.9 15.4 1.0 CE1 C:HIS179 3.0 16.4 1.0 OD2 C:ASP177 3.0 15.7 1.0 CG C:HIS179 3.1 14.3 1.0 OD1 C:ASP265 3.3 15.1 1.0 CB C:HIS179 3.5 13.8 1.0 N C:HIS179 3.8 13.4 1.0 C1 C:ZL4410 3.8 16.5 1.0 C3 C:ZL4410 3.9 16.8 1.0 C4 C:ZL4410 3.9 17.4 1.0 CA C:GLY302 4.0 15.3 1.0 NE2 C:HIS179 4.1 16.1 1.0 CG2 C:ILE178 4.2 15.2 1.0 CD2 C:HIS179 4.2 15.1 1.0 CB C:ASP177 4.2 14.0 1.0 OH C:TYR304 4.2 16.8 1.0 CB C:ASP265 4.3 14.1 1.0 CA C:HIS179 4.3 13.6 1.0 N C:ILE178 4.3 14.1 1.0 CE2 C:TYR304 4.4 16.9 1.0 NE2 C:HIS141 4.4 16.2 1.0 N C:GLY302 4.4 14.5 1.0 C C:ILE178 4.8 13.5 1.0 CZ C:TYR304 4.8 17.3 1.0 CE1 C:HIS141 4.8 17.3 1.0 C C:ZL4410 4.8 16.9 1.0 C C:ASP177 4.9 14.9 1.0 NE2 C:HIS142 4.9 15.4 1.0 CA C:ASP177 4.9 14.3 1.0 CA C:ILE178 5.0 13.7 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