Calcium in PDB 6wbz: Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
Enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
All present enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group:
3.5.1.98;
Protein crystallography data
The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group, PDB code: 6wbz
was solved by
D.J.Klein,
W.Yu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.26 /
1.32
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.390,
99.170,
139.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
19.2
|
Other elements in 6wbz:
The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
(pdb code 6wbz). 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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group, PDB code: 6wbz:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6wbz
Go back to
Calcium Binding Sites List in 6wbz
Calcium binding site 1 out
of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:28.5
occ:1.00
|
O
|
A:ASP177
|
2.8
|
13.8
|
1.0
|
OD1
|
A:ASP175
|
2.8
|
13.0
|
1.0
|
O
|
A:PHE199
|
2.8
|
14.0
|
1.0
|
OG
|
A:SER198
|
2.9
|
14.7
|
1.0
|
O
|
A:HIS179
|
2.9
|
12.9
|
1.0
|
O
|
A:ASP175
|
3.0
|
12.9
|
1.0
|
CG
|
A:ASP175
|
3.4
|
13.1
|
1.0
|
C
|
A:ASP175
|
3.6
|
12.9
|
1.0
|
C
|
A:PHE199
|
3.7
|
15.6
|
1.0
|
C
|
A:ASP177
|
3.7
|
13.6
|
1.0
|
N
|
A:ASP177
|
3.8
|
11.2
|
1.0
|
N
|
A:PHE199
|
3.8
|
12.8
|
1.0
|
C
|
A:HIS179
|
3.8
|
14.2
|
1.0
|
CB
|
A:HIS200
|
3.8
|
13.3
|
1.0
|
CB
|
A:ASP175
|
3.8
|
13.4
|
1.0
|
CB
|
A:SER198
|
4.0
|
13.9
|
1.0
|
CB
|
A:ASP177
|
4.1
|
12.7
|
1.0
|
N
|
A:GLY181
|
4.1
|
13.5
|
1.0
|
CA
|
A:ASP177
|
4.2
|
10.7
|
1.0
|
OD2
|
A:ASP175
|
4.2
|
14.2
|
1.0
|
CA
|
A:HIS180
|
4.2
|
12.4
|
1.0
|
ND1
|
A:HIS200
|
4.2
|
14.8
|
1.0
|
N
|
A:ILE176
|
4.2
|
11.2
|
1.0
|
CA
|
A:SER198
|
4.3
|
12.2
|
1.0
|
C
|
A:ILE176
|
4.3
|
12.8
|
1.0
|
CA
|
A:ASP175
|
4.3
|
12.0
|
1.0
|
CA
|
A:HIS200
|
4.4
|
13.0
|
1.0
|
C
|
A:SER198
|
4.4
|
13.8
|
1.0
|
N
|
A:HIS180
|
4.4
|
12.8
|
1.0
|
N
|
A:HIS200
|
4.4
|
13.2
|
1.0
|
CA
|
A:ILE176
|
4.4
|
11.2
|
1.0
|
C
|
A:HIS180
|
4.5
|
14.1
|
1.0
|
CA
|
A:PHE199
|
4.5
|
12.4
|
1.0
|
CG
|
A:HIS200
|
4.5
|
14.2
|
1.0
|
N
|
A:HIS179
|
4.6
|
11.7
|
1.0
|
C
|
A:ILE178
|
4.7
|
13.6
|
1.0
|
CA
|
A:HIS179
|
4.8
|
12.4
|
1.0
|
N
|
A:ILE178
|
4.8
|
12.1
|
1.0
|
O
|
A:HOH589
|
4.9
|
16.3
|
1.0
|
CE1
|
A:HIS141
|
4.9
|
13.1
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6wbz
Go back to
Calcium Binding Sites List in 6wbz
Calcium binding site 2 out
of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca407
b:36.0
occ:1.00
|
O
|
A:PHE188
|
2.7
|
17.6
|
1.0
|
O
|
A:VAL194
|
2.7
|
18.6
|
1.0
|
O
|
A:HOH530
|
2.8
|
18.6
|
1.0
|
O
|
A:HOH738
|
2.9
|
19.4
|
1.0
|
O
|
A:THR191
|
3.0
|
18.8
|
1.0
|
O
|
A:TYR223
|
3.2
|
16.6
|
1.0
|
C
|
A:PHE188
|
3.6
|
17.9
|
1.0
|
CB
|
A:TYR223
|
3.7
|
16.8
|
1.0
|
C
|
A:TYR223
|
3.8
|
17.6
|
1.0
|
C
|
A:VAL194
|
3.8
|
17.9
|
1.0
|
CB
|
A:PHE188
|
4.1
|
15.4
|
1.0
|
C
|
A:THR191
|
4.2
|
19.7
|
1.0
|
CA
|
A:TYR223
|
4.3
|
16.5
|
1.0
|
CA
|
A:TYR189
|
4.4
|
16.7
|
1.0
|
N
|
A:TYR189
|
4.4
|
16.7
|
1.0
|
O
|
A:TYR189
|
4.5
|
18.5
|
1.0
|
C
|
A:TYR189
|
4.5
|
19.9
|
1.0
|
CA
|
A:PHE188
|
4.5
|
14.7
|
1.0
|
CA
|
A:MET195
|
4.5
|
14.8
|
1.0
|
N
|
A:ALA224
|
4.6
|
15.8
|
1.0
|
N
|
A:THR191
|
4.6
|
18.8
|
1.0
|
N
|
A:THR196
|
4.6
|
14.1
|
1.0
|
N
|
A:MET195
|
4.7
|
14.5
|
1.0
|
CG2
|
A:THR191
|
4.7
|
22.2
|
1.0
|
O
|
A:GLY220
|
4.7
|
17.3
|
1.0
|
OG1
|
A:THR196
|
4.7
|
15.2
|
1.0
|
CA
|
A:VAL194
|
4.8
|
15.4
|
1.0
|
CB
|
A:VAL194
|
4.8
|
17.2
|
1.0
|
CA
|
A:GLY220
|
4.8
|
18.0
|
1.0
|
CG2
|
A:THR196
|
4.9
|
14.4
|
1.0
|
CA
|
A:THR191
|
4.9
|
18.3
|
1.0
|
CG
|
A:TYR223
|
4.9
|
16.9
|
1.0
|
N
|
A:VAL194
|
5.0
|
16.2
|
1.0
|
CA
|
A:ALA224
|
5.0
|
15.8
|
1.0
|
CB
|
A:ALA224
|
5.0
|
16.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6wbz
Go back to
Calcium Binding Sites List in 6wbz
Calcium binding site 3 out
of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca404
b:28.1
occ:1.00
|
O
|
B:ASP177
|
2.8
|
12.1
|
1.0
|
OD1
|
B:ASP175
|
2.8
|
12.4
|
1.0
|
O
|
B:PHE199
|
2.8
|
11.8
|
1.0
|
OG
|
B:SER198
|
2.9
|
13.6
|
1.0
|
O
|
B:HIS179
|
2.9
|
11.8
|
1.0
|
O
|
B:ASP175
|
3.0
|
12.3
|
1.0
|
CG
|
B:ASP175
|
3.4
|
11.9
|
1.0
|
C
|
B:ASP175
|
3.6
|
12.1
|
1.0
|
C
|
B:PHE199
|
3.7
|
12.0
|
1.0
|
C
|
B:ASP177
|
3.7
|
11.5
|
1.0
|
N
|
B:ASP177
|
3.8
|
10.7
|
1.0
|
CB
|
B:HIS200
|
3.8
|
11.9
|
1.0
|
N
|
B:PHE199
|
3.8
|
11.8
|
1.0
|
C
|
B:HIS179
|
3.8
|
12.3
|
1.0
|
CB
|
B:ASP175
|
3.8
|
11.6
|
1.0
|
CB
|
B:SER198
|
4.0
|
13.7
|
1.0
|
CB
|
B:ASP177
|
4.1
|
10.8
|
1.0
|
CA
|
B:ASP177
|
4.2
|
10.5
|
1.0
|
OD2
|
B:ASP175
|
4.2
|
14.4
|
1.0
|
N
|
B:ILE176
|
4.2
|
10.1
|
1.0
|
ND1
|
B:HIS200
|
4.2
|
13.6
|
1.0
|
N
|
B:GLY181
|
4.2
|
12.8
|
1.0
|
CA
|
B:HIS180
|
4.2
|
12.4
|
1.0
|
C
|
B:ILE176
|
4.3
|
11.3
|
1.0
|
CA
|
B:SER198
|
4.3
|
12.2
|
1.0
|
CA
|
B:ASP175
|
4.3
|
10.8
|
1.0
|
CA
|
B:HIS200
|
4.4
|
11.2
|
1.0
|
CA
|
B:ILE176
|
4.4
|
10.2
|
1.0
|
N
|
B:HIS180
|
4.4
|
12.5
|
1.0
|
C
|
B:SER198
|
4.4
|
14.0
|
1.0
|
N
|
B:HIS200
|
4.4
|
11.7
|
1.0
|
CA
|
B:PHE199
|
4.5
|
11.1
|
1.0
|
CG
|
B:HIS200
|
4.5
|
12.9
|
1.0
|
C
|
B:HIS180
|
4.5
|
13.0
|
1.0
|
N
|
B:HIS179
|
4.6
|
10.3
|
1.0
|
C
|
B:ILE178
|
4.7
|
11.6
|
1.0
|
N
|
B:ILE178
|
4.8
|
10.0
|
1.0
|
O
|
B:HOH593
|
4.8
|
13.5
|
1.0
|
CA
|
B:HIS179
|
4.9
|
11.2
|
1.0
|
CE1
|
B:HIS141
|
4.9
|
12.2
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6wbz
Go back to
Calcium Binding Sites List in 6wbz
Calcium binding site 4 out
of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca405
b:35.6
occ:1.00
|
O
|
B:PHE188
|
2.7
|
16.6
|
1.0
|
O
|
B:VAL194
|
2.7
|
17.1
|
1.0
|
O
|
B:HOH604
|
2.7
|
19.0
|
1.0
|
O
|
B:HOH747
|
2.9
|
17.9
|
1.0
|
O
|
B:THR191
|
3.0
|
18.5
|
1.0
|
O
|
B:TYR223
|
3.2
|
17.1
|
1.0
|
CB
|
B:TYR223
|
3.6
|
16.8
|
1.0
|
C
|
B:PHE188
|
3.6
|
15.8
|
1.0
|
C
|
B:TYR223
|
3.8
|
18.2
|
1.0
|
C
|
B:VAL194
|
3.8
|
16.3
|
1.0
|
CB
|
B:PHE188
|
4.1
|
16.1
|
1.0
|
C
|
B:THR191
|
4.2
|
19.0
|
1.0
|
CA
|
B:TYR223
|
4.3
|
15.3
|
1.0
|
CA
|
B:TYR189
|
4.4
|
15.6
|
1.0
|
N
|
B:TYR189
|
4.4
|
15.6
|
1.0
|
O
|
B:TYR189
|
4.4
|
18.2
|
1.0
|
C
|
B:TYR189
|
4.5
|
18.9
|
1.0
|
CA
|
B:MET195
|
4.5
|
13.3
|
1.0
|
CA
|
B:PHE188
|
4.5
|
15.3
|
1.0
|
N
|
B:ALA224
|
4.6
|
15.3
|
1.0
|
N
|
B:THR191
|
4.6
|
18.4
|
1.0
|
N
|
B:THR196
|
4.6
|
13.2
|
1.0
|
N
|
B:MET195
|
4.6
|
14.1
|
1.0
|
CG2
|
B:THR191
|
4.7
|
18.6
|
1.0
|
OG1
|
B:THR196
|
4.7
|
15.0
|
1.0
|
O
|
B:GLY220
|
4.7
|
18.2
|
1.0
|
CA
|
B:VAL194
|
4.8
|
14.2
|
1.0
|
CB
|
B:VAL194
|
4.8
|
16.3
|
1.0
|
CA
|
B:GLY220
|
4.9
|
19.1
|
1.0
|
CG
|
B:TYR223
|
4.9
|
18.5
|
1.0
|
CA
|
B:THR191
|
4.9
|
17.8
|
1.0
|
N
|
B:VAL194
|
4.9
|
15.7
|
1.0
|
CG2
|
B:THR196
|
4.9
|
14.7
|
1.0
|
CA
|
B:ALA224
|
5.0
|
14.8
|
1.0
|
C
|
B:MET195
|
5.0
|
14.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6wbz
Go back to
Calcium Binding Sites List in 6wbz
Calcium binding site 5 out
of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca406
b:35.6
occ:1.00
|
O
|
C:VAL194
|
2.6
|
18.3
|
1.0
|
O
|
C:PHE188
|
2.6
|
16.9
|
1.0
|
O
|
C:HOH513
|
2.7
|
20.3
|
1.0
|
O
|
C:THR191
|
2.8
|
17.6
|
1.0
|
O
|
C:HOH713
|
3.0
|
18.6
|
1.0
|
O
|
C:TYR223
|
3.2
|
17.8
|
1.0
|
C
|
C:PHE188
|
3.6
|
16.4
|
1.0
|
CB
|
C:TYR223
|
3.7
|
17.8
|
1.0
|
C
|
C:VAL194
|
3.7
|
18.8
|
1.0
|
C
|
C:TYR223
|
3.8
|
18.4
|
1.0
|
C
|
C:THR191
|
4.0
|
19.3
|
1.0
|
CB
|
C:PHE188
|
4.1
|
16.5
|
1.0
|
CA
|
C:TYR223
|
4.3
|
17.6
|
1.0
|
CA
|
C:TYR189
|
4.4
|
15.7
|
1.0
|
N
|
C:TYR189
|
4.4
|
15.4
|
1.0
|
O
|
C:TYR189
|
4.4
|
17.1
|
1.0
|
CA
|
C:MET195
|
4.5
|
18.3
|
1.0
|
C
|
C:TYR189
|
4.5
|
17.9
|
1.0
|
N
|
C:THR191
|
4.5
|
16.2
|
1.0
|
CA
|
C:PHE188
|
4.5
|
14.6
|
1.0
|
N
|
C:ALA224
|
4.6
|
18.3
|
1.0
|
N
|
C:MET195
|
4.6
|
17.7
|
1.0
|
N
|
C:THR196
|
4.6
|
15.2
|
1.0
|
CG2
|
C:THR191
|
4.6
|
17.4
|
1.0
|
O
|
C:GLY220
|
4.7
|
18.6
|
1.0
|
CA
|
C:VAL194
|
4.7
|
16.0
|
1.0
|
OG1
|
C:THR196
|
4.7
|
16.6
|
1.0
|
CA
|
C:THR191
|
4.8
|
16.5
|
1.0
|
CB
|
C:VAL194
|
4.8
|
18.1
|
1.0
|
CA
|
C:GLY220
|
4.8
|
18.2
|
1.0
|
N
|
C:VAL194
|
4.9
|
16.9
|
1.0
|
CG
|
C:TYR223
|
4.9
|
18.3
|
1.0
|
CG2
|
C:THR196
|
4.9
|
15.8
|
1.0
|
C
|
C:MET195
|
5.0
|
16.5
|
1.0
|
CA
|
C:ALA224
|
5.0
|
17.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6wbz
Go back to
Calcium Binding Sites List in 6wbz
Calcium binding site 6 out
of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group
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 An Ethyl Ketone Inhibitor Containing A Spiro-Bicyclic Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca407
b:33.4
occ:1.00
|
O
|
C:ASP177
|
2.7
|
16.1
|
1.0
|
OD1
|
C:ASP175
|
2.8
|
16.9
|
1.0
|
OG
|
C:SER198
|
2.9
|
17.4
|
1.0
|
O
|
C:HIS179
|
2.9
|
15.2
|
1.0
|
O
|
C:PHE199
|
2.9
|
17.0
|
1.0
|
O
|
C:ASP175
|
3.0
|
15.6
|
1.0
|
CG
|
C:ASP175
|
3.4
|
18.3
|
1.0
|
C
|
C:ASP175
|
3.6
|
16.8
|
1.0
|
C
|
C:ASP177
|
3.7
|
17.8
|
1.0
|
N
|
C:ASP177
|
3.7
|
15.8
|
1.0
|
C
|
C:PHE199
|
3.7
|
16.4
|
1.0
|
C
|
C:HIS179
|
3.8
|
15.2
|
1.0
|
CB
|
C:HIS200
|
3.8
|
15.0
|
1.0
|
N
|
C:PHE199
|
3.8
|
16.3
|
1.0
|
CB
|
C:ASP175
|
3.8
|
14.9
|
1.0
|
CB
|
C:SER198
|
4.0
|
16.0
|
1.0
|
CB
|
C:ASP177
|
4.1
|
15.2
|
1.0
|
CA
|
C:ASP177
|
4.1
|
15.2
|
1.0
|
OD2
|
C:ASP175
|
4.2
|
16.5
|
1.0
|
N
|
C:GLY181
|
4.2
|
15.9
|
1.0
|
CA
|
C:HIS180
|
4.2
|
14.6
|
1.0
|
N
|
C:ILE176
|
4.2
|
15.6
|
1.0
|
C
|
C:ILE176
|
4.3
|
18.0
|
1.0
|
CA
|
C:SER198
|
4.3
|
14.8
|
1.0
|
ND1
|
C:HIS200
|
4.3
|
17.6
|
1.0
|
CA
|
C:ASP175
|
4.3
|
14.0
|
1.0
|
C
|
C:SER198
|
4.4
|
17.3
|
1.0
|
CA
|
C:HIS200
|
4.4
|
14.0
|
1.0
|
N
|
C:HIS180
|
4.4
|
14.5
|
1.0
|
CA
|
C:ILE176
|
4.4
|
15.3
|
1.0
|
N
|
C:HIS200
|
4.5
|
14.6
|
1.0
|
C
|
C:HIS180
|
4.5
|
16.7
|
1.0
|
CA
|
C:PHE199
|
4.5
|
15.3
|
1.0
|
CG
|
C:HIS200
|
4.5
|
16.1
|
1.0
|
N
|
C:HIS179
|
4.5
|
15.5
|
1.0
|
C
|
C:ILE178
|
4.7
|
17.2
|
1.0
|
N
|
C:ILE178
|
4.8
|
16.1
|
1.0
|
CA
|
C:HIS179
|
4.8
|
15.3
|
1.0
|
O
|
C:HOH594
|
4.9
|
18.8
|
1.0
|
CE1
|
C:HIS141
|
4.9
|
16.2
|
1.0
|
|
Reference:
W.Yu,
J.Liu,
Y.Yu,
V.Zhang,
D.Clausen,
J.Kelly,
S.Wolkenberg,
D.Beshore,
J.L.Duffy,
C.C.Chang,
R.W.Myers,
D.J.Klein,
J.Fells,
K.Holloway,
J.Wu,
G.Wu,
B.J.Howell,
R.J.O.Barnard,
J.Kozlowski.
Discovery of Ethyl Ketone-Based Hdacs 1, 2, and 3 Selective Inhibitors For Hiv Latency Reactivation. Bioorg.Med.Chem.Lett. 27197 2020.
ISSN: ESSN 1464-3405
PubMed: 32331932
DOI: 10.1016/J.BMCL.2020.127197
Page generated: Tue Jul 16 17:24:13 2024
|