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Zinc in PDB 7kbh: Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16)

Enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16)

All present enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16), PDB code: 7kbh 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) 46.20 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.41, 98.8, 139.55, 90, 90, 90
R / Rfree (%) 15 / 22.1

Other elements in 7kbh:

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16) 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 A 2-Substituted Benzamide Inhibitor (Compound 16) (pdb code 7kbh). 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 16), PDB code: 7kbh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7kbh

Go back to Zinc Binding Sites List in 7kbh
Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16)


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

b:29.9
occ:1.00
 OD1 A:ASP177 1.9 23.0 1.0
OD2 A:ASP266 2.0 25.4 1.0
ND1 A:HIS179 2.0 30.6 1.0
O1 A:WB4407 2.2 50.1 1.0
CG A:ASP177 2.8 23.6 1.0
CE1 A:HIS179 2.9 31.2 1.0
OD2 A:ASP177 3.0 22.8 1.0
CG A:ASP266 3.0 23.1 1.0
CG A:HIS179 3.1 30.5 1.0
C22 A:WB4407 3.3 49.6 1.0
OD1 A:ASP266 3.4 23.0 1.0
CB A:HIS179 3.5 29.5 1.0
N A:HIS179 3.9 25.5 1.0
NE2 A:HIS141 3.9 28.3 1.0
C23 A:WB4407 3.9 49.6 1.0
NE2 A:HIS179 4.1 31.6 1.0
CA A:GLY303 4.1 25.4 1.0
C28 A:WB4407 4.1 49.3 1.0
CB A:ASP177 4.2 20.4 1.0
CD2 A:HIS179 4.2 31.6 1.0
CA A:HIS179 4.3 25.9 1.0
NE2 A:HIS142 4.4 22.7 1.0
CB A:ASP266 4.4 23.9 1.0
N4 A:WB4407 4.4 49.3 1.0
CE1 A:HIS141 4.4 27.1 1.0
N A:GLY303 4.4 26.1 1.0
CG2 A:ILE178 4.4 26.9 1.0
C29 A:WB4407 4.5 49.4 1.0
N A:ILE178 4.5 23.2 1.0
C21 A:WB4407 4.7 49.0 1.0
C24 A:WB4407 4.8 49.8 1.0
C A:ILE178 4.9 25.1 1.0

Zinc binding site 2 out of 3 in 7kbh

Go back to Zinc Binding Sites List in 7kbh
Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16)


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

b:25.1
occ:1.00
 OD2 B:ASP266 1.9 28.7 1.0
O B:HOH522 2.0 24.4 1.0
OD1 B:ASP177 2.0 13.8 1.0
ND1 B:HIS179 2.1 22.0 1.0
O1 B:WB4406 2.4 43.5 1.0
CG B:ASP177 2.7 14.6 1.0
OD2 B:ASP177 2.8 13.3 1.0
CG B:ASP266 2.9 27.2 1.0
CE1 B:HIS179 3.0 22.5 1.0
CG B:HIS179 3.3 21.6 1.0
C22 B:WB4406 3.3 43.8 1.0
OD1 B:ASP266 3.3 25.5 1.0
CB B:HIS179 3.7 19.7 1.0
C23 B:WB4406 4.0 44.2 1.0
N B:HIS179 4.0 18.1 1.0
CA B:GLY303 4.0 26.5 1.0
N4 B:WB4406 4.2 43.9 1.0
CB B:ASP177 4.2 12.9 1.0
NE2 B:HIS179 4.2 22.6 1.0
CB B:ASP266 4.2 25.2 1.0
NE2 B:HIS141 4.3 23.9 1.0
CG2 B:ILE178 4.3 22.1 1.0
C28 B:WB4406 4.3 43.9 1.0
CD2 B:HIS179 4.3 22.7 1.0
C21 B:WB4406 4.4 44.6 1.0
NE2 B:HIS142 4.4 21.9 1.0
N B:GLY303 4.4 25.7 1.0
N B:ILE178 4.5 24.1 1.0
CA B:HIS179 4.5 17.7 1.0
C29 B:WB4406 4.5 45.0 1.0
CE1 B:HIS141 4.8 22.8 1.0
C24 B:WB4406 4.9 44.4 1.0
C B:ASP177 4.9 25.8 1.0
CA B:ASP177 4.9 23.8 1.0
C B:ILE178 4.9 27.6 1.0

Zinc binding site 3 out of 3 in 7kbh

Go back to Zinc Binding Sites List in 7kbh
Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 16)


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

b:36.6
occ:1.00
 O1 C:WB4405 1.9 52.8 1.0
OD1 C:ASP177 1.9 31.9 1.0
OD2 C:ASP266 2.1 46.0 1.0
ND1 C:HIS179 2.2 29.7 1.0
CG C:ASP177 2.8 32.5 1.0
OD2 C:ASP177 3.0 34.7 1.0
C22 C:WB4405 3.1 52.0 1.0
CE1 C:HIS179 3.1 27.1 1.0
CG C:ASP266 3.1 47.5 1.0
CG C:HIS179 3.2 27.4 1.0
OD1 C:ASP266 3.5 46.5 1.0
CB C:HIS179 3.5 24.5 1.0
N C:HIS179 3.7 37.1 1.0
NE2 C:HIS141 3.9 32.6 1.0
C23 C:WB4405 4.0 52.0 1.0
N4 C:WB4405 4.0 51.3 1.0
C21 C:WB4405 4.1 51.2 1.0
CA C:GLY303 4.2 27.3 1.0
CB C:ASP177 4.2 29.9 1.0
C28 C:WB4405 4.2 52.0 1.0
CA C:HIS179 4.2 37.9 1.0
CE1 C:HIS141 4.3 32.0 1.0
NE2 C:HIS179 4.3 27.2 1.0
NE2 C:HIS142 4.3 33.0 1.0
N C:ILE178 4.3 23.4 1.0
CD2 C:HIS179 4.3 27.8 1.0
CG2 C:ILE178 4.4 26.2 1.0
CB C:ASP266 4.5 45.7 1.0
N C:GLY303 4.5 27.4 1.0
C29 C:WB4405 4.7 51.5 1.0
C C:ILE178 4.7 25.4 1.0
CA C:ILE178 4.9 23.3 1.0
C C:ASP177 4.9 40.6 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 22:06:00 2024

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