Zinc in PDB 6wbz: Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group

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

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group:
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, PDB code: 6wbz 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) 19.26 / 1.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.390, 99.170, 139.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.2

Other elements in 6wbz:

The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group 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 (pdb code 6wbz). 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, PDB code: 6wbz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6wbz

Go back to Zinc Binding Sites List in 6wbz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:13.3
occ:1.00
 OD2 A:ASP265 1.9 14.3 1.0
OD1 A:ASP177 2.0 12.7 1.0
O1 A:TV7411 2.0 13.7 1.0
ND1 A:HIS179 2.0 12.5 1.0
O A:TV7411 2.5 13.0 1.0
C2 A:TV7411 2.7 15.5 1.0
CG A:ASP177 2.8 13.3 1.0
CG A:ASP265 2.9 12.9 1.0
CE1 A:HIS179 2.9 14.9 1.0
OD2 A:ASP177 3.0 13.3 1.0
CG A:HIS179 3.2 12.8 1.0
OD1 A:ASP265 3.3 13.8 1.0
CB A:HIS179 3.6 12.1 1.0
C3 A:TV7411 3.8 15.1 1.0
N A:HIS179 3.8 11.7 1.0
C1 A:TV7411 3.8 17.1 1.0
C4 A:TV7411 3.9 15.1 1.0
CA A:GLY302 4.0 13.4 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 12.7 1.0
CD2 A:HIS179 4.2 14.5 1.0
CB A:ASP265 4.3 12.7 1.0
OH A:TYR304 4.3 14.4 1.0
CA A:HIS179 4.3 12.4 1.0
CE2 A:TYR304 4.4 13.8 1.0
N A:ILE178 4.4 12.1 1.0
NE2 A:HIS141 4.4 13.0 1.0
N A:GLY302 4.4 13.0 1.0
C A:TV7411 4.8 19.5 1.0
CZ A:TYR304 4.8 12.9 1.0
C A:ILE178 4.8 13.6 1.0
CE1 A:HIS141 4.8 13.1 1.0
NE2 A:HIS142 4.9 14.4 1.0
CA A:ASP177 4.9 10.7 1.0
C A:ASP177 5.0 13.6 1.0
CA A:ILE178 5.0 12.0 1.0

Zinc binding site 2 out of 3 in 6wbz

Go back to Zinc Binding Sites List in 6wbz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:12.2
occ:1.00
 OD1 B:ASP177 2.0 11.4 1.0
OD2 B:ASP265 2.0 11.8 1.0
ND1 B:HIS179 2.0 11.9 1.0
O1 B:TV7408 2.0 12.6 1.0
O B:TV7408 2.4 11.9 1.0
C2 B:TV7408 2.8 13.8 1.0
CG B:ASP177 2.8 12.0 1.0
CE1 B:HIS179 2.9 12.3 1.0
CG B:ASP265 2.9 11.8 1.0
OD2 B:ASP177 3.1 11.7 1.0
CG B:HIS179 3.1 12.2 1.0
OD1 B:ASP265 3.3 11.1 1.0
CB B:HIS179 3.6 11.7 1.0
C1 B:TV7408 3.8 15.9 1.0
N B:HIS179 3.8 10.3 1.0
C3 B:TV7408 3.8 12.9 1.0
C4 B:TV7408 3.9 13.6 1.0
CA B:GLY302 4.0 12.3 1.0
NE2 B:HIS179 4.1 12.7 1.0
CG2 B:ILE178 4.2 12.2 1.0
CD2 B:HIS179 4.2 13.3 1.0
CB B:ASP177 4.3 10.8 1.0
CB B:ASP265 4.3 11.5 1.0
OH B:TYR304 4.3 13.2 1.0
CA B:HIS179 4.3 11.2 1.0
NE2 B:HIS141 4.4 13.1 1.0
N B:ILE178 4.4 10.0 1.0
CE2 B:TYR304 4.4 11.9 1.0
N B:GLY302 4.4 11.3 1.0
C B:ILE178 4.8 11.6 1.0
C B:TV7408 4.8 16.6 1.0
CE1 B:HIS141 4.9 12.2 1.0
CZ B:TYR304 4.9 12.1 1.0
C B:ASP177 4.9 11.5 1.0
CA B:ASP177 4.9 10.5 1.0
NE2 B:HIS142 4.9 13.5 1.0

Zinc binding site 3 out of 3 in 6wbz

Go back to Zinc Binding Sites List in 6wbz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:16.6
occ:1.00
 OD1 C:ASP177 2.0 14.7 1.0
OD2 C:ASP265 2.0 16.5 1.0
O1 C:TV7410 2.0 16.9 1.0
ND1 C:HIS179 2.1 16.8 1.0
O C:TV7410 2.4 16.8 1.0
C2 C:TV7410 2.7 18.8 1.0
CG C:ASP177 2.8 13.7 1.0
CG C:ASP265 3.0 17.5 1.0
CE1 C:HIS179 3.0 16.6 1.0
OD2 C:ASP177 3.0 16.7 1.0
CG C:HIS179 3.2 15.9 1.0
OD1 C:ASP265 3.3 17.3 1.0
CB C:HIS179 3.6 14.6 1.0
C1 C:TV7410 3.8 19.2 1.0
N C:HIS179 3.8 15.5 1.0
C3 C:TV7410 3.8 15.5 1.0
C4 C:TV7410 3.9 18.2 1.0
CA C:GLY302 4.0 16.5 1.0
NE2 C:HIS179 4.1 16.5 1.0
CG2 C:ILE178 4.2 17.1 1.0
CB C:ASP177 4.2 15.2 1.0
CD2 C:HIS179 4.2 15.9 1.0
OH C:TYR304 4.3 17.2 1.0
CB C:ASP265 4.3 16.4 1.0
CA C:HIS179 4.3 15.3 1.0
N C:ILE178 4.4 16.1 1.0
NE2 C:HIS141 4.4 16.5 1.0
CE2 C:TYR304 4.4 19.6 1.0
N C:GLY302 4.4 16.6 1.0
CE1 C:HIS141 4.8 16.2 1.0
C C:ILE178 4.8 17.2 1.0
CZ C:TYR304 4.8 20.6 1.0
C C:TV7410 4.8 20.8 1.0
NE2 C:HIS142 4.9 16.0 1.0
C C:ASP177 4.9 17.8 1.0
CA C:ASP177 5.0 15.2 1.0
CA C:ILE178 5.0 14.7 1.0

Reference:

W.Yu, J.Liu, Y.Yu, V.Zhang, D.Clausen, J.Kelly, S.Wolkenberg, D.Beshore, J.L.Duffy, C.C.Chang, R.W.Myers, D.J.Klein, J.Fells, K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Discovery of Ethyl Ketone-Based Hdacs 1, 2, and 3 Selective Inhibitors For Hiv Latency Reactivation. Bioorg.Med.Chem.Lett. 27197 2020.
ISSN: ESSN 1464-3405
PubMed: 32331932
DOI: 10.1016/J.BMCL.2020.127197
Page generated: Tue Oct 29 09:18:53 2024

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