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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7moz:

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

Calcium (Ca) 6 atoms

Zinc Binding Sites:

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 7moz

Go back to Zinc Binding Sites List in 7moz
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 7moz

Go back to Zinc Binding Sites List in 7moz
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 7moz

Go back to Zinc Binding Sites List in 7moz
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

Reference:

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
Page generated: Sun Aug 22 09:48:39 2021

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