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: Tue Oct 29 21:20:25 2024

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