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: Sun Aug 22 09:46:21 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy