Zinc in PDB 7kbg: Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)

Enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)

All present enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg was solved by D.J.Klein, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.08 / 1.26
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.26, 99.27, 139.02, 90, 90, 90
R / Rfree (%) 18.4 / 19.6

Other elements in 7kbg:

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Chlorine (Cl) 2 atoms
Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) (pdb code 7kbg). 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 A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7kbg

Go back to Zinc Binding Sites List in 7kbg
Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


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 A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:12.0
occ:1.00
 O1 A:WBA411 2.0 13.1 1.0
OD2 A:ASP265 2.0 11.8 1.0
OD1 A:ASP177 2.0 11.1 1.0
ND1 A:HIS179 2.0 12.1 1.0
O2 A:WBA411 2.2 12.4 1.0
CG A:ASP177 2.8 10.9 1.0
CE1 A:HIS179 2.9 12.6 1.0
OD2 A:ASP177 3.0 11.2 1.0
CG A:ASP265 3.0 12.3 1.0
C24 A:WBA411 3.0 12.6 1.0
C22 A:WBA411 3.0 12.2 1.0
CG A:HIS179 3.2 11.5 1.0
OD1 A:ASP265 3.4 12.4 1.0
C23 A:WBA411 3.5 12.3 1.0
CB A:HIS179 3.6 12.0 1.0
CA A:GLY302 4.0 11.9 1.0
N A:HIS179 4.0 11.4 1.0
N4 A:WBA411 4.1 13.1 1.0
NE2 A:HIS141 4.1 12.2 1.0
NE2 A:HIS179 4.1 12.5 1.0
C25 A:WBA411 4.1 12.9 1.0
N A:GLY302 4.2 11.6 1.0
CD2 A:HIS179 4.2 11.9 1.0
CB A:ASP177 4.2 11.5 1.0
CG2 A:ILE178 4.3 12.8 1.0
CB A:ASP265 4.3 12.5 1.0
NE2 A:HIS142 4.4 13.1 1.0
CA A:HIS179 4.4 11.2 1.0
N A:ILE178 4.6 11.6 1.0
C21 A:WBA411 4.6 14.3 1.0
CE1 A:HIS141 4.7 11.4 1.0
OH A:TYR304 4.7 14.2 1.0
C28 A:WBA411 4.8 12.5 1.0
CE2 A:TYR304 4.9 12.2 1.0

Zinc binding site 2 out of 3 in 7kbg

Go back to Zinc Binding Sites List in 7kbg
Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


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 A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:10.7
occ:1.00
 OD2 B:ASP265 2.0 10.6 1.0
O1 B:WBA409 2.0 10.6 1.0
ND1 B:HIS179 2.0 10.3 1.0
OD1 B:ASP177 2.0 9.6 1.0
O2 B:WBA409 2.3 10.6 1.0
CG B:ASP177 2.9 9.8 1.0
CE1 B:HIS179 2.9 11.0 1.0
CG B:ASP265 3.0 10.4 1.0
C24 B:WBA409 3.0 10.8 1.0
OD2 B:ASP177 3.0 10.5 1.0
C22 B:WBA409 3.1 10.9 1.0
CG B:HIS179 3.1 10.4 1.0
OD1 B:ASP265 3.3 10.2 1.0
C23 B:WBA409 3.5 10.6 1.0
CB B:HIS179 3.6 11.0 1.0
CA B:GLY302 4.0 10.6 1.0
N B:HIS179 4.0 10.6 1.0
NE2 B:HIS141 4.1 11.5 1.0
N4 B:WBA409 4.1 11.8 1.0
C25 B:WBA409 4.1 11.0 1.0
NE2 B:HIS179 4.1 12.0 1.0
N B:GLY302 4.2 10.0 1.0
CD2 B:HIS179 4.2 11.8 1.0
CB B:ASP177 4.3 9.6 1.0
CB B:ASP265 4.3 10.0 1.0
CG2 B:ILE178 4.3 11.0 1.0
NE2 B:HIS142 4.4 12.3 1.0
CA B:HIS179 4.4 10.6 1.0
N B:ILE178 4.6 10.2 1.0
C21 B:WBA409 4.6 12.0 1.0
CE1 B:HIS141 4.7 10.7 1.0
OH B:TYR304 4.7 13.0 1.0
C28 B:WBA409 4.8 11.5 1.0
CE2 B:TYR304 4.9 11.5 1.0

Zinc binding site 3 out of 3 in 7kbg

Go back to Zinc Binding Sites List in 7kbg
Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


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 A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:13.3
occ:1.00
 O1 C:WBA412 1.9 13.0 1.0
OD2 C:ASP265 2.0 13.2 1.0
OD1 C:ASP177 2.0 11.7 1.0
ND1 C:HIS179 2.1 13.2 1.0
O2 C:WBA412 2.2 13.7 1.0
CG C:ASP177 2.8 10.9 1.0
CE1 C:HIS179 2.9 14.4 1.0
CG C:ASP265 3.0 13.0 1.0
OD2 C:ASP177 3.0 12.9 1.0
C24 C:WBA412 3.0 12.5 1.0
C22 C:WBA412 3.0 13.5 1.0
CG C:HIS179 3.2 12.5 1.0
OD1 C:ASP265 3.4 13.1 1.0
C23 C:WBA412 3.4 12.6 1.0
CB C:HIS179 3.6 12.1 1.0
CA C:GLY302 4.0 13.6 1.0
N C:HIS179 4.0 12.1 1.0
N4 C:WBA412 4.1 14.4 1.0
NE2 C:HIS141 4.1 13.6 1.0
NE2 C:HIS179 4.1 13.8 1.0
C25 C:WBA412 4.1 12.6 1.0
N C:GLY302 4.2 13.0 1.0
CD2 C:HIS179 4.3 13.1 1.0
CB C:ASP177 4.3 12.0 1.0
CB C:ASP265 4.3 12.5 1.0
CG2 C:ILE178 4.3 13.3 1.0
NE2 C:HIS142 4.3 13.6 1.0
CA C:HIS179 4.5 12.1 1.0
N C:ILE178 4.5 12.4 1.0
C21 C:WBA412 4.6 14.5 1.0
CE1 C:HIS141 4.7 13.4 1.0
OH C:TYR304 4.7 17.2 1.0
C28 C:WBA412 4.8 12.8 1.0
CE2 C:TYR304 4.9 16.3 1.0

Reference:

J.Liu, Y.Yu, J.Kelly, D.Sha, A.B.Alhassan, W.Yu, M.M.Maletic, J.L.Duffy, D.J.Klein, M.K.Holloway, S.Carroll, B.J.Howell, R.J.O.Barnard, S.Wolkenberg, J.A.Kozlowski. Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on A 2-Substituted Benzamide Zinc Binding Group. Acs Med.Chem.Lett. V. 11 2476 2020.
ISSN: ISSN 1948-5875
PubMed: 33335670
DOI: 10.1021/ACSMEDCHEMLETT.0C00462
Page generated: Mon Jan 25 16:46:10 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