Calcium 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:

Zinc (Zn) 3 atoms
Chlorine (Cl) 2 atoms
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7kbg

Go back to Calcium Binding Sites List in 7kbg
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca402

b:26.4
occ:1.00
 OD1 A:ASP175 2.8 11.7 1.0
O A:ASP177 2.8 12.1 1.0
O A:PHE199 2.9 12.2 1.0
O A:HIS179 2.9 12.1 1.0
OG A:SER198 2.9 12.2 1.0
O A:ASP175 3.0 11.6 1.0
CG A:ASP175 3.4 11.9 1.0
C A:ASP175 3.6 11.2 1.0
C A:PHE199 3.6 12.3 1.0
N A:PHE199 3.7 12.0 1.0
C A:ASP177 3.7 11.3 1.0
CB A:HIS200 3.8 12.1 1.0
C A:HIS179 3.8 11.7 1.0
N A:ASP177 3.8 11.0 1.0
CB A:ASP175 3.8 11.8 1.0
CB A:SER198 4.0 12.4 1.0
OD2 A:ASP175 4.1 12.9 1.0
CB A:ASP177 4.1 11.5 1.0
CA A:ASP177 4.2 11.0 1.0
N A:GLY181 4.2 11.6 1.0
ND1 A:HIS200 4.2 13.1 1.0
CA A:SER198 4.2 12.0 1.0
N A:ILE176 4.3 11.0 1.0
CA A:HIS180 4.3 12.0 1.0
C A:ILE176 4.3 11.0 1.0
C A:SER198 4.3 12.0 1.0
CA A:ASP175 4.4 11.2 1.0
CA A:HIS200 4.4 12.2 1.0
N A:HIS200 4.4 11.9 1.0
CA A:PHE199 4.4 12.1 1.0
N A:HIS180 4.4 12.0 1.0
CA A:ILE176 4.5 11.4 1.0
CG A:HIS200 4.5 11.8 1.0
C A:HIS180 4.5 11.9 1.0
N A:HIS179 4.5 11.4 1.0
C A:ILE178 4.7 11.2 1.0
CA A:HIS179 4.8 11.2 1.0
CE1 A:HIS141 4.8 11.4 1.0
N A:ILE178 4.8 11.6 1.0
O A:HOH563 4.9 13.7 1.0

Calcium binding site 2 out of 6 in 7kbg

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Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca403

b:31.0
occ:1.00
 O A:PHE188 2.7 15.1 1.0
O A:VAL194 2.7 15.7 1.0
O A:HOH572 2.7 17.3 1.0
O A:THR191 2.9 16.2 1.0
O A:HOH707 2.9 16.4 1.0
O A:TYR223 3.2 14.9 1.0
C A:PHE188 3.6 14.7 1.0
CB A:TYR223 3.6 14.9 1.0
C A:TYR223 3.8 14.6 1.0
C A:VAL194 3.8 15.0 1.0
CB A:PHE188 4.1 14.3 1.0
C A:THR191 4.1 15.7 1.0
CA A:TYR223 4.3 15.0 1.0
CA A:TYR189 4.4 15.0 1.0
N A:TYR189 4.4 15.4 1.0
O A:TYR189 4.4 16.8 1.0
C A:TYR189 4.5 16.2 1.0
CA A:PHE188 4.5 14.7 1.0
CA A:MET195 4.5 14.2 1.0
N A:THR191 4.5 16.5 1.0
N A:ALA224 4.6 14.6 1.0
CG2 A:THR191 4.6 17.1 1.0
N A:MET195 4.6 14.2 1.0
N A:THR196 4.7 12.6 1.0
O A:GLY220 4.7 16.4 1.0
OG1 A:THR196 4.7 14.0 1.0
CA A:GLY220 4.8 17.6 1.0
CA A:VAL194 4.8 14.7 1.0
CB A:VAL194 4.8 14.8 1.0
CA A:THR191 4.9 16.2 1.0
CG A:TYR223 4.9 15.3 1.0
CG2 A:THR196 4.9 14.2 1.0
N A:VAL194 4.9 14.8 1.0
CA A:ALA224 5.0 15.0 1.0

Calcium binding site 3 out of 6 in 7kbg

Go back to Calcium Binding Sites List in 7kbg
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
B:Ca402

b:25.9
occ:1.00
 O B:ASP177 2.8 10.5 1.0
OD1 B:ASP175 2.8 10.7 1.0
O B:HIS179 2.8 10.8 1.0
O B:PHE199 2.8 10.9 1.0
OG B:SER198 2.9 11.9 1.0
O B:ASP175 3.1 10.2 1.0
CG B:ASP175 3.4 10.4 1.0
C B:ASP175 3.6 10.1 1.0
C B:PHE199 3.7 10.8 1.0
C B:ASP177 3.7 10.5 1.0
C B:HIS179 3.7 10.6 1.0
CB B:HIS200 3.7 11.6 1.0
N B:ASP177 3.8 10.1 1.0
N B:PHE199 3.8 10.6 1.0
CB B:ASP175 3.9 10.7 1.0
CB B:SER198 4.0 11.2 1.0
CB B:ASP177 4.1 9.6 1.0
CA B:ASP177 4.1 9.8 1.0
OD2 B:ASP175 4.2 11.6 1.0
ND1 B:HIS200 4.2 12.0 1.0
CA B:HIS180 4.3 10.9 1.0
N B:GLY181 4.3 11.6 1.0
N B:ILE176 4.3 9.4 1.0
C B:ILE176 4.3 9.9 1.0
CA B:SER198 4.3 10.8 1.0
CA B:HIS200 4.3 11.0 1.0
N B:HIS180 4.4 10.7 1.0
CA B:ASP175 4.4 10.0 1.0
N B:HIS200 4.4 11.5 1.0
C B:SER198 4.4 11.3 1.0
CA B:PHE199 4.5 10.8 1.0
CG B:HIS200 4.5 11.8 1.0
CA B:ILE176 4.5 9.7 1.0
N B:HIS179 4.5 10.6 1.0
C B:HIS180 4.5 11.4 1.0
C B:ILE178 4.6 10.8 1.0
CA B:HIS179 4.7 10.6 1.0
N B:ILE178 4.8 10.2 1.0
CE1 B:HIS141 4.8 10.7 1.0
O B:HOH585 4.8 12.3 1.0
O B:ILE178 5.0 10.8 1.0

Calcium binding site 4 out of 6 in 7kbg

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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:Ca403

b:30.3
occ:1.00
 O B:PHE188 2.6 14.7 1.0
O B:VAL194 2.7 14.9 1.0
O B:HOH580 2.8 16.3 1.0
O B:HOH742 2.9 15.1 1.0
O B:THR191 2.9 15.3 1.0
O B:TYR223 3.2 13.8 1.0
C B:PHE188 3.6 13.7 1.0
CB B:TYR223 3.6 14.7 1.0
C B:VAL194 3.8 13.9 1.0
C B:TYR223 3.8 14.3 1.0
CB B:PHE188 4.1 13.6 1.0
C B:THR191 4.1 15.6 1.0
CA B:TYR223 4.3 14.7 1.0
CA B:TYR189 4.4 15.1 1.0
N B:TYR189 4.4 14.2 1.0
O B:TYR189 4.4 15.6 1.0
C B:TYR189 4.5 15.8 1.0
CA B:MET195 4.5 13.3 1.0
CA B:PHE188 4.5 14.0 1.0
N B:ALA224 4.6 14.0 1.0
N B:THR191 4.6 15.8 1.0
N B:MET195 4.6 13.3 1.0
N B:THR196 4.6 12.2 1.0
CG2 B:THR191 4.7 17.3 1.0
O B:GLY220 4.7 16.4 1.0
OG1 B:THR196 4.7 13.4 1.0
CA B:VAL194 4.7 13.2 1.0
CB B:VAL194 4.8 13.4 1.0
CA B:GLY220 4.8 17.4 1.0
CA B:THR191 4.9 16.0 1.0
N B:VAL194 4.9 13.3 1.0
CG B:TYR223 4.9 15.1 1.0
CG2 B:THR196 5.0 13.7 1.0
C B:MET195 5.0 12.6 1.0
CA B:ALA224 5.0 13.5 1.0

Calcium binding site 5 out of 6 in 7kbg

Go back to Calcium Binding Sites List in 7kbg
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca403

b:30.2
occ:1.00
 O C:PHE188 2.6 13.7 1.0
O C:VAL194 2.6 15.4 1.0
O C:HOH558 2.8 18.1 1.0
O C:THR191 2.9 14.9 1.0
O C:HOH729 2.9 15.7 1.0
O C:TYR223 3.2 15.3 1.0
C C:PHE188 3.6 12.9 1.0
CB C:TYR223 3.7 15.3 1.0
C C:VAL194 3.8 15.0 1.0
C C:TYR223 3.8 15.4 1.0
CB C:PHE188 4.1 13.2 1.0
C C:THR191 4.1 14.6 1.0
CA C:TYR223 4.4 15.4 1.0
N C:TYR189 4.4 14.0 1.0
CA C:TYR189 4.4 15.0 1.0
O C:TYR189 4.4 14.5 1.0
C C:TYR189 4.4 14.5 1.0
CA C:PHE188 4.5 13.1 1.0
CA C:MET195 4.5 14.2 1.0
N C:THR191 4.5 14.2 1.0
N C:ALA224 4.5 14.9 1.0
CG2 C:THR191 4.6 15.2 1.0
N C:MET195 4.6 14.2 1.0
N C:THR196 4.6 12.9 1.0
O C:GLY220 4.7 16.0 1.0
CA C:VAL194 4.8 14.1 1.0
OG1 C:THR196 4.8 14.0 1.0
CA C:GLY220 4.8 15.7 1.0
CA C:THR191 4.8 14.5 1.0
CB C:VAL194 4.8 14.1 1.0
N C:VAL194 4.9 14.0 1.0
C C:MET195 4.9 13.6 1.0
CG C:TYR223 5.0 16.1 1.0
CG2 C:THR196 5.0 13.6 1.0
CA C:ALA224 5.0 14.8 1.0

Calcium binding site 6 out of 6 in 7kbg

Go back to Calcium Binding Sites List in 7kbg
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca404

b:27.7
occ:1.00
 O C:ASP177 2.7 13.4 1.0
OD1 C:ASP175 2.8 13.6 1.0
O C:HIS179 2.8 12.4 1.0
O C:PHE199 2.9 13.3 1.0
OG C:SER198 3.0 13.2 1.0
O C:ASP175 3.0 12.5 1.0
CG C:ASP175 3.4 13.6 1.0
C C:ASP175 3.6 12.0 1.0
C C:ASP177 3.7 13.2 1.0
C C:PHE199 3.7 12.6 1.0
N C:ASP177 3.7 13.0 1.0
C C:HIS179 3.7 11.8 1.0
CB C:HIS200 3.8 13.4 1.0
N C:PHE199 3.8 12.9 1.0
CB C:ASP175 3.9 12.0 1.0
CB C:ASP177 4.0 12.0 1.0
CA C:ASP177 4.1 12.6 1.0
CB C:SER198 4.1 13.0 1.0
OD2 C:ASP175 4.2 13.4 1.0
C C:ILE176 4.2 13.6 1.0
N C:ILE176 4.3 12.2 1.0
N C:GLY181 4.3 12.4 1.0
ND1 C:HIS200 4.3 13.6 1.0
CA C:SER198 4.3 12.4 1.0
CA C:HIS180 4.3 12.3 1.0
CA C:ASP175 4.4 11.6 1.0
CA C:HIS200 4.4 13.2 1.0
N C:HIS180 4.4 12.1 1.0
C C:SER198 4.4 12.7 1.0
N C:HIS200 4.4 12.9 1.0
CA C:ILE176 4.4 13.2 1.0
N C:HIS179 4.4 12.1 1.0
CA C:PHE199 4.5 12.6 1.0
CG C:HIS200 4.5 12.8 1.0
C C:HIS180 4.6 12.3 1.0
C C:ILE178 4.6 12.6 1.0
CA C:HIS179 4.7 12.1 1.0
N C:ILE178 4.7 12.4 1.0
O C:HOH574 4.8 15.6 1.0
CE1 C:HIS141 4.8 13.4 1.0
O C:ILE178 5.0 12.5 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: Sun Jan 24 09:40:34 2021

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