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Calcium 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:

Zinc (Zn) 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 16) (pdb code 7kbh). 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 16), PDB code: 7kbh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7kbh

Go back to Calcium Binding Sites List in 7kbh
Calcium binding site 1 out of 6 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 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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:34.0
occ:1.00
 O A:HIS179 2.6 28.6 1.0
O A:PHE199 2.8 28.2 1.0
O A:ASP177 2.8 23.8 1.0
OD1 A:ASP175 2.9 26.7 1.0
OG A:SER198 3.0 26.6 1.0
O A:ASP175 3.0 31.2 1.0
CG A:ASP175 3.3 26.4 1.0
C A:ASP175 3.6 32.4 1.0
N A:ASP177 3.6 22.2 1.0
CB A:ASP175 3.7 24.2 1.0
C A:PHE199 3.7 29.2 1.0
C A:HIS179 3.7 29.4 1.0
C A:ASP177 3.7 24.6 1.0
CB A:HIS200 3.8 20.1 1.0
N A:PHE199 4.0 27.1 1.0
CB A:ASP177 4.0 20.4 1.0
CA A:ASP177 4.1 22.0 1.0
OD2 A:ASP175 4.1 25.2 1.0
CA A:HIS180 4.2 31.8 1.0
C A:ILE176 4.2 28.3 1.0
CB A:SER198 4.2 24.4 1.0
CA A:ASP175 4.3 30.0 1.0
CA A:HIS200 4.3 19.7 1.0
N A:ILE176 4.3 27.5 1.0
N A:GLY181 4.3 25.8 1.0
N A:HIS180 4.3 33.1 1.0
N A:HIS200 4.3 20.2 1.0
ND1 A:HIS200 4.4 22.2 1.0
CA A:ILE176 4.5 26.1 1.0
CA A:PHE199 4.6 26.1 1.0
C A:SER198 4.6 29.1 1.0
CA A:SER198 4.6 25.5 1.0
CG A:HIS200 4.6 21.9 1.0
C A:HIS180 4.6 33.2 1.0
N A:HIS179 4.6 25.5 1.0
O A:HOH540 4.6 21.4 1.0
C A:ILE178 4.7 25.1 1.0
CA A:HIS179 4.8 25.9 1.0
N A:ILE178 4.8 23.2 1.0
CE1 A:HIS141 4.9 27.1 1.0
O A:ILE178 5.0 25.3 1.0

Calcium binding site 2 out of 6 in 7kbh

Go back to Calcium Binding Sites List in 7kbh
Calcium binding site 2 out of 6 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 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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:41.7
occ:1.00
 O A:PHE188 2.4 29.1 1.0
O A:VAL194 2.6 27.9 1.0
O A:HOH512 2.7 31.0 1.0
O A:HOH564 2.9 14.8 1.0
O A:THR191 3.0 25.9 1.0
O A:TYR224 3.2 31.3 1.0
C A:PHE188 3.5 29.6 1.0
CB A:TYR224 3.6 30.0 1.0
C A:VAL194 3.8 26.4 1.0
C A:TYR224 3.8 32.0 1.0
CB A:PHE188 4.1 23.5 1.0
C A:THR191 4.2 26.0 1.0
CA A:TYR189 4.3 31.7 1.0
N A:TYR189 4.3 32.2 1.0
CA A:TYR224 4.3 29.1 1.0
C A:TYR189 4.4 36.2 1.0
O A:TYR189 4.4 35.5 1.0
CA A:MET195 4.5 21.9 1.0
N A:THR191 4.5 25.5 1.0
CA A:PHE188 4.5 26.3 1.0
N A:THR196 4.6 28.1 1.0
N A:MET195 4.6 22.4 1.0
CG2 A:THR191 4.6 28.6 1.0
N A:ALA225 4.6 31.2 1.0
O A:GLY221 4.6 40.1 1.0
OG1 A:THR196 4.7 23.0 1.0
CA A:VAL194 4.8 24.7 1.0
CA A:THR191 4.9 24.7 1.0
CA A:GLY221 4.9 39.4 1.0
CG A:TYR224 4.9 29.5 1.0
N A:THR190 5.0 35.6 1.0
CG2 A:THR196 5.0 24.3 1.0
CA A:ALA225 5.0 30.2 1.0

Calcium binding site 3 out of 6 in 7kbh

Go back to Calcium Binding Sites List in 7kbh
Calcium binding site 3 out of 6 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 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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:29.9
occ:1.00
 OD1 B:ASP175 2.6 23.6 1.0
O B:ASP177 2.6 25.7 1.0
O B:PHE199 2.7 21.0 1.0
O B:HIS179 2.8 19.6 1.0
OG B:SER198 2.9 17.8 1.0
O B:ASP175 3.3 32.3 1.0
CG B:ASP175 3.4 23.1 1.0
C B:PHE199 3.5 21.8 1.0
N B:PHE199 3.6 19.9 1.0
C B:ASP175 3.7 31.6 1.0
C B:ASP177 3.7 25.8 1.0
N B:ASP177 3.7 23.1 1.0
CB B:ASP175 3.7 22.3 1.0
C B:HIS179 3.8 21.1 1.0
CB B:HIS200 3.8 20.8 1.0
CB B:SER198 4.1 17.2 1.0
N B:ILE176 4.1 33.2 1.0
ND1 B:HIS200 4.2 23.5 1.0
CA B:ASP177 4.2 23.8 1.0
N B:HIS200 4.2 27.0 1.0
C B:SER198 4.2 28.4 1.0
CB B:ASP177 4.2 12.9 1.0
C B:ILE176 4.2 33.4 1.0
CA B:PHE199 4.2 18.6 1.0
CA B:SER198 4.3 24.2 1.0
CA B:HIS200 4.3 26.6 1.0
CA B:ILE176 4.3 32.1 1.0
CA B:ASP175 4.3 28.9 1.0
CA B:HIS180 4.4 22.9 1.0
OD2 B:ASP175 4.5 24.7 1.0
N B:HIS180 4.5 23.7 1.0
N B:GLY181 4.5 21.5 1.0
N B:HIS179 4.5 18.1 1.0
CG B:HIS200 4.5 22.8 1.0
O B:HOH516 4.6 15.6 1.0
C B:ILE178 4.7 27.6 1.0
CA B:HIS179 4.8 17.7 1.0
C B:HIS180 4.8 23.8 1.0
N B:ILE178 4.8 24.1 1.0

Calcium binding site 4 out of 6 in 7kbh

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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 16)


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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:33.3
occ:1.00
 O B:VAL194 2.5 36.9 1.0
O B:HOH524 2.6 33.7 1.0
O B:PHE188 2.6 44.0 1.0
O B:HOH528 2.8 21.7 1.0
O B:TYR224 2.8 33.5 1.0
O B:THR191 3.0 29.5 1.0
C B:PHE188 3.6 44.1 1.0
C B:TYR224 3.6 34.9 1.0
CB B:TYR224 3.7 31.9 1.0
C B:VAL194 3.7 36.7 1.0
CB B:PHE188 4.1 23.9 1.0
C B:THR191 4.2 29.3 1.0
CA B:TYR224 4.3 31.6 1.0
CA B:TYR189 4.3 27.1 1.0
N B:TYR189 4.3 27.0 1.0
CA B:MET195 4.4 24.9 1.0
N B:ALA225 4.5 18.7 1.0
CA B:PHE188 4.5 41.4 1.0
N B:MET195 4.5 25.2 1.0
C B:TYR189 4.5 29.1 1.0
N B:THR191 4.5 28.0 1.0
N B:THR196 4.6 27.8 1.0
OG1 B:THR196 4.6 29.4 1.0
CG2 B:THR191 4.6 23.9 1.0
O B:GLY221 4.7 39.9 1.0
O B:TYR189 4.7 28.8 1.0
CA B:VAL194 4.8 33.2 1.0
C B:MET195 4.9 26.8 1.0
CA B:THR191 4.9 27.1 1.0
CA B:ALA225 4.9 19.5 1.0
CB B:VAL194 4.9 26.4 1.0
CG2 B:THR196 4.9 28.6 1.0
N B:VAL194 4.9 34.4 1.0
CB B:ALA225 5.0 24.8 1.0
CA B:GLY221 5.0 42.0 1.0

Calcium binding site 5 out of 6 in 7kbh

Go back to Calcium Binding Sites List in 7kbh
Calcium binding site 5 out of 6 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 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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:36.9
occ:1.00
 O C:HOH507 2.5 33.6 1.0
O C:PHE188 2.6 26.7 1.0
O C:VAL194 2.8 31.9 1.0
O C:HOH538 2.9 31.5 1.0
O C:TYR224 3.0 29.7 1.0
O C:THR191 3.0 31.7 1.0
C C:PHE188 3.6 28.1 1.0
CB C:TYR224 3.6 20.2 1.0
C C:TYR224 3.6 29.6 1.0
C C:VAL194 4.0 32.7 1.0
CB C:PHE188 4.1 25.0 1.0
CA C:TYR224 4.2 26.7 1.0
C C:THR191 4.2 33.6 1.0
CA C:TYR189 4.3 35.3 1.0
N C:TYR189 4.3 35.8 1.0
O C:TYR189 4.4 39.7 1.0
C C:TYR189 4.4 39.7 1.0
N C:ALA225 4.4 33.1 1.0
CA C:MET195 4.5 27.1 1.0
CA C:PHE188 4.5 26.2 1.0
N C:THR196 4.5 29.9 1.0
N C:THR191 4.6 30.0 1.0
O C:GLY221 4.6 38.8 1.0
N C:MET195 4.7 26.9 1.0
OG1 C:THR196 4.7 24.8 1.0
CG2 C:THR196 4.7 23.0 1.0
CG2 C:THR191 4.8 26.3 1.0
CB C:ALA225 4.8 15.9 1.0
CA C:ALA225 4.8 32.4 1.0
CA C:GLY221 4.8 36.6 1.0
CG C:TYR224 4.9 20.7 1.0
CA C:THR191 4.9 29.8 1.0
C C:MET195 5.0 29.8 1.0

Calcium binding site 6 out of 6 in 7kbh

Go back to Calcium Binding Sites List in 7kbh
Calcium binding site 6 out of 6 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 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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:42.8
occ:1.00
 OD1 C:ASP175 2.6 35.5 1.0
O C:ASP177 2.7 39.9 1.0
O C:HIS179 2.8 38.6 1.0
O C:PHE199 2.8 36.0 1.0
OG C:SER198 3.1 27.2 1.0
O C:ASP175 3.2 36.2 1.0
CG C:ASP175 3.3 37.3 1.0
C C:ASP177 3.6 40.6 1.0
C C:PHE199 3.7 35.4 1.0
C C:ASP175 3.7 35.4 1.0
CB C:ASP175 3.7 33.0 1.0
C C:HIS179 3.7 39.0 1.0
N C:ASP177 3.7 39.0 1.0
CB C:HIS200 3.8 27.8 1.0
N C:PHE199 4.0 34.2 1.0
CB C:ASP177 4.0 29.9 1.0
CA C:ASP177 4.1 37.4 1.0
OD2 C:ASP175 4.3 35.3 1.0
C C:ILE176 4.3 29.9 1.0
CA C:HIS200 4.3 22.6 1.0
CB C:SER198 4.3 26.2 1.0
N C:ILE176 4.3 25.9 1.0
CA C:ASP175 4.3 32.3 1.0
CA C:HIS180 4.3 31.6 1.0
N C:HIS180 4.4 31.9 1.0
N C:HIS200 4.4 22.2 1.0
ND1 C:HIS200 4.5 30.6 1.0
N C:HIS179 4.5 37.1 1.0
N C:GLY181 4.5 27.6 1.0
CA C:ILE176 4.5 26.0 1.0
CA C:PHE199 4.5 34.2 1.0
C C:SER198 4.5 30.0 1.0
CA C:SER198 4.6 26.8 1.0
CG C:HIS200 4.6 29.9 1.0
C C:ILE178 4.6 25.4 1.0
N C:ILE178 4.7 23.4 1.0
O C:HOH532 4.7 29.2 1.0
C C:HIS180 4.7 34.0 1.0
CA C:HIS179 4.7 37.9 1.0
O C:ILE178 5.0 25.9 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: Fri Jul 19 01:14:59 2024

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