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Zinc in PDB 7js8: Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22)

Enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22)

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22), PDB code: 7js8 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) 23.60 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.43, 99.16, 139.65, 90, 90, 90
R / Rfree (%) 16.7 / 19

Other elements in 7js8:

The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22) also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22) (pdb code 7js8). 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 Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22), PDB code: 7js8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7js8

Go back to Zinc Binding Sites List in 7js8
Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22)


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 Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.7
occ:1.00
 OD2 A:ASP265 1.9 16.5 1.0
OD1 A:ASP177 2.0 16.1 1.0
ND1 A:HIS179 2.0 16.3 1.0
O1 A:VJV411 2.1 18.9 1.0
O A:VJV411 2.5 17.7 1.0
C2 A:VJV411 2.8 19.7 1.0
CG A:ASP177 2.8 15.4 1.0
CG A:ASP265 2.9 15.6 1.0
CE1 A:HIS179 2.9 17.2 1.0
OD2 A:ASP177 3.0 16.8 1.0
CG A:HIS179 3.1 15.8 1.0
OD1 A:ASP265 3.3 14.7 1.0
CB A:HIS179 3.5 15.5 1.0
C1 A:VJV411 3.8 21.2 1.0
N A:HIS179 3.8 14.8 1.0
C3 A:VJV411 3.9 20.4 1.0
C4 A:VJV411 3.9 20.9 1.0
CA A:GLY302 4.0 15.9 1.0
NE2 A:HIS179 4.1 17.4 1.0
CG2 A:ILE178 4.1 14.9 1.0
CB A:ASP177 4.2 14.5 1.0
CD2 A:HIS179 4.2 16.4 1.0
CB A:ASP265 4.2 15.9 1.0
N A:ILE178 4.3 13.5 1.0
CA A:HIS179 4.3 15.1 1.0
OH A:TYR304 4.3 17.0 1.0
CE2 A:TYR304 4.4 15.8 1.0
NE2 A:HIS141 4.4 18.2 1.0
N A:GLY302 4.4 15.3 1.0
C A:ILE178 4.8 15.7 1.0
CZ A:TYR304 4.9 16.4 1.0
C A:VJV411 4.9 21.7 1.0
CE1 A:HIS141 4.9 18.5 1.0
C A:ASP177 4.9 14.7 1.0
CA A:ASP177 4.9 13.8 1.0
NE2 A:HIS142 4.9 17.7 1.0
CA A:ILE178 5.0 14.3 1.0

Zinc binding site 2 out of 3 in 7js8

Go back to Zinc Binding Sites List in 7js8
Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22)


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 Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:15.4
occ:1.00
 OD2 B:ASP265 1.9 16.1 1.0
OD1 B:ASP177 2.0 14.4 1.0
ND1 B:HIS179 2.0 13.7 1.0
O B:VJV408 2.0 17.5 1.0
O1 B:VJV408 2.5 16.4 1.0
C2 B:VJV408 2.7 17.9 1.0
CG B:ASP177 2.8 15.5 1.0
CE1 B:HIS179 2.9 15.3 1.0
CG B:ASP265 2.9 15.0 1.0
OD2 B:ASP177 3.0 14.9 1.0
CG B:HIS179 3.1 14.5 1.0
OD1 B:ASP265 3.3 13.6 1.0
CB B:HIS179 3.6 13.7 1.0
C1 B:VJV408 3.8 19.6 1.0
N B:HIS179 3.8 13.5 1.0
C3 B:VJV408 3.8 18.5 1.0
C4 B:VJV408 3.9 18.8 1.0
CA B:GLY302 4.0 14.2 1.0
NE2 B:HIS179 4.1 16.3 1.0
CG2 B:ILE178 4.2 13.9 1.0
CD2 B:HIS179 4.2 15.6 1.0
CB B:ASP177 4.2 13.3 1.0
CB B:ASP265 4.3 14.2 1.0
CA B:HIS179 4.3 13.4 1.0
OH B:TYR304 4.3 16.1 1.0
N B:ILE178 4.4 11.5 1.0
CE2 B:TYR304 4.4 14.5 1.0
N B:GLY302 4.4 13.0 1.0
NE2 B:HIS141 4.4 16.8 1.0
C B:VJV408 4.8 20.0 1.0
C B:ILE178 4.8 13.3 1.0
CZ B:TYR304 4.9 14.2 1.0
CE1 B:HIS141 4.9 17.1 1.0
C B:ASP177 4.9 12.8 1.0
CA B:ASP177 4.9 12.5 1.0
NE2 B:HIS142 5.0 17.2 1.0
CA B:ILE178 5.0 12.1 1.0

Zinc binding site 3 out of 3 in 7js8

Go back to Zinc Binding Sites List in 7js8
Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22)


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 Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:21.2
occ:1.00
 OD1 C:ASP177 1.9 18.7 1.0
OD2 C:ASP265 2.0 21.6 1.0
ND1 C:HIS179 2.0 21.7 1.0
O1 C:VJV410 2.1 23.1 1.0
O C:VJV410 2.5 21.6 1.0
CG C:ASP177 2.8 19.9 1.0
C2 C:VJV410 2.8 23.3 1.0
CG C:ASP265 2.9 22.2 1.0
CE1 C:HIS179 3.0 21.6 1.0
OD2 C:ASP177 3.0 21.1 1.0
CG C:HIS179 3.1 19.4 1.0
OD1 C:ASP265 3.2 21.3 1.0
CB C:HIS179 3.5 18.9 1.0
N C:HIS179 3.8 19.0 1.0
C1 C:VJV410 3.8 24.2 1.0
C3 C:VJV410 3.9 23.6 1.0
C4 C:VJV410 3.9 24.6 1.0
CA C:GLY302 4.0 21.5 1.0
NE2 C:HIS179 4.2 21.0 1.0
CG2 C:ILE178 4.2 20.9 1.0
CB C:ASP177 4.2 19.9 1.0
CD2 C:HIS179 4.2 19.8 1.0
OH C:TYR304 4.3 23.1 1.0
CB C:ASP265 4.3 21.1 1.0
CA C:HIS179 4.3 18.7 1.0
N C:ILE178 4.3 19.5 1.0
CE2 C:TYR304 4.4 24.1 1.0
NE2 C:HIS141 4.4 22.5 1.0
N C:GLY302 4.4 21.0 1.0
C C:ILE178 4.8 19.4 1.0
CZ C:TYR304 4.8 24.6 1.0
C C:VJV410 4.9 24.7 1.0
CE1 C:HIS141 4.9 22.8 1.0
C C:ASP177 4.9 20.1 1.0
CA C:ASP177 4.9 20.0 1.0
NE2 C:HIS142 5.0 21.1 1.0
CA C:ILE178 5.0 19.3 1.0

Reference:

W.Yu, J.Liu, D.Clausen, Y.Yu, J.L.Duffy, M.Wang, S.Xu, L.Deng, T.Suzuki, C.C.Chung, R.W.Myers, D.J.Klein, J.I.Fells, M.K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Discovery of Ethyl Ketone-Based Highly Selective Hdacs 1, 2, 3 Inhibitors For Hiv Latency Reactivation with Minimum Cellular Potency Serum Shift and Reduced Herg Activity. J.Med.Chem. V. 64 4709 2021.
ISSN: ISSN 0022-2623
PubMed: 33797924
DOI: 10.1021/ACS.JMEDCHEM.0C02150
Page generated: Fri Aug 22 00:54:45 2025

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