Zinc in PDB 7ltk: Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)
Enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)
All present enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12):
3.5.1.98;
Protein crystallography data
The structure of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12), PDB code: 7ltk
was solved by
D.J.Klein,
D.C.Beshore,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.20 /
1.59
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.16,
98.43,
139.2,
90,
90,
90
|
R / Rfree (%)
|
17.2 /
19.8
|
Other elements in 7ltk:
The structure of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)
(pdb code 7ltk). 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 An Inhibitor That Lacks A Zinc Binding Group (Compound 12), PDB code: 7ltk:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 7ltk
Go back to
Zinc Binding Sites List in 7ltk
Zinc binding site 1 out
of 3 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)
![](/pictures/ZN/pdb/lt/7ltk-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/lt/7ltk-ZN-sphere_01_stereo.jpg) 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 An Inhibitor That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:21.0
occ:1.00
|
OD2
|
A:ASP265
|
1.8
|
19.4
|
1.0
|
OD1
|
A:ASP177
|
2.0
|
20.1
|
1.0
|
ND1
|
A:HIS179
|
2.1
|
21.7
|
1.0
|
O
|
A:ACT404
|
2.1
|
24.2
|
1.0
|
OXT
|
A:ACT404
|
2.3
|
28.3
|
1.0
|
C
|
A:ACT404
|
2.5
|
28.2
|
1.0
|
CG
|
A:ASP177
|
2.8
|
20.3
|
1.0
|
CG
|
A:ASP265
|
2.9
|
18.2
|
1.0
|
OD2
|
A:ASP177
|
2.9
|
19.0
|
1.0
|
CE1
|
A:HIS179
|
3.0
|
21.3
|
1.0
|
CG
|
A:HIS179
|
3.2
|
21.0
|
1.0
|
OD1
|
A:ASP265
|
3.2
|
18.1
|
1.0
|
CB
|
A:HIS179
|
3.6
|
19.6
|
1.0
|
N
|
A:HIS179
|
3.9
|
18.4
|
1.0
|
CH3
|
A:ACT404
|
4.1
|
28.7
|
1.0
|
CA
|
A:GLY302
|
4.1
|
18.7
|
1.0
|
NE2
|
A:HIS141
|
4.2
|
22.1
|
1.0
|
NE2
|
A:HIS179
|
4.2
|
21.2
|
1.0
|
CG2
|
A:ILE178
|
4.2
|
20.8
|
1.0
|
CB
|
A:ASP177
|
4.2
|
17.8
|
1.0
|
CB
|
A:ASP265
|
4.2
|
20.2
|
1.0
|
CD2
|
A:HIS179
|
4.3
|
21.1
|
1.0
|
CA
|
A:HIS179
|
4.3
|
18.3
|
1.0
|
C17
|
A:YEM408
|
4.3
|
25.9
|
1.0
|
N
|
A:GLY302
|
4.4
|
19.3
|
1.0
|
N
|
A:ILE178
|
4.4
|
18.4
|
1.0
|
NE2
|
A:HIS142
|
4.6
|
23.0
|
1.0
|
CE1
|
A:HIS141
|
4.6
|
21.4
|
1.0
|
CE2
|
A:TYR304
|
4.6
|
21.3
|
1.0
|
OH
|
A:TYR304
|
4.6
|
23.8
|
1.0
|
C
|
A:ASP177
|
4.9
|
20.4
|
1.0
|
C
|
A:ILE178
|
4.9
|
21.8
|
1.0
|
CA
|
A:ASP177
|
4.9
|
16.9
|
1.0
|
|
Zinc binding site 2 out
of 3 in 7ltk
Go back to
Zinc Binding Sites List in 7ltk
Zinc binding site 2 out
of 3 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)
![](/pictures/ZN/pdb/lt/7ltk-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/lt/7ltk-ZN-sphere_02_stereo.jpg) 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 An Inhibitor That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:19.4
occ:1.00
|
OD2
|
B:ASP265
|
1.9
|
19.2
|
1.0
|
OD1
|
B:ASP177
|
2.0
|
20.1
|
1.0
|
ND1
|
B:HIS179
|
2.0
|
19.5
|
1.0
|
OXT
|
B:ACT404
|
2.3
|
26.9
|
1.0
|
O
|
B:ACT404
|
2.3
|
25.8
|
1.0
|
C
|
B:ACT404
|
2.6
|
25.0
|
1.0
|
CG
|
B:ASP177
|
2.8
|
20.6
|
1.0
|
CG
|
B:ASP265
|
2.9
|
18.5
|
1.0
|
CE1
|
B:HIS179
|
2.9
|
20.5
|
1.0
|
OD2
|
B:ASP177
|
2.9
|
16.8
|
1.0
|
CG
|
B:HIS179
|
3.1
|
19.6
|
1.0
|
OD1
|
B:ASP265
|
3.2
|
18.3
|
1.0
|
CB
|
B:HIS179
|
3.5
|
17.2
|
1.0
|
N
|
B:HIS179
|
3.9
|
17.2
|
1.0
|
CA
|
B:GLY302
|
4.1
|
15.9
|
1.0
|
NE2
|
B:HIS179
|
4.1
|
20.7
|
1.0
|
CH3
|
B:ACT404
|
4.1
|
24.4
|
1.0
|
NE2
|
B:HIS141
|
4.2
|
19.9
|
1.0
|
CD2
|
B:HIS179
|
4.2
|
21.3
|
1.0
|
CB
|
B:ASP177
|
4.2
|
16.9
|
1.0
|
CG2
|
B:ILE178
|
4.2
|
17.3
|
1.0
|
CB
|
B:ASP265
|
4.2
|
17.7
|
1.0
|
C17
|
B:YEM407
|
4.3
|
27.3
|
1.0
|
CA
|
B:HIS179
|
4.3
|
15.6
|
1.0
|
N
|
B:GLY302
|
4.4
|
15.8
|
1.0
|
N
|
B:ILE178
|
4.4
|
15.6
|
1.0
|
CE2
|
B:TYR304
|
4.5
|
16.9
|
1.0
|
NE2
|
B:HIS142
|
4.6
|
21.2
|
1.0
|
OH
|
B:TYR304
|
4.6
|
23.0
|
1.0
|
CE1
|
B:HIS141
|
4.7
|
19.6
|
1.0
|
C
|
B:ILE178
|
4.9
|
18.6
|
1.0
|
C
|
B:ASP177
|
4.9
|
17.9
|
1.0
|
CA
|
B:ASP177
|
4.9
|
15.6
|
1.0
|
|
Zinc binding site 3 out
of 3 in 7ltk
Go back to
Zinc Binding Sites List in 7ltk
Zinc binding site 3 out
of 3 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)
![](/pictures/ZN/pdb/lt/7ltk-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/lt/7ltk-ZN-sphere_03_stereo.jpg) 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 An Inhibitor That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:25.8
occ:1.00
|
OD1
|
C:ASP177
|
1.9
|
23.8
|
1.0
|
OD2
|
C:ASP265
|
2.0
|
26.1
|
1.0
|
ND1
|
C:HIS179
|
2.0
|
26.4
|
1.0
|
O
|
C:ACT404
|
2.2
|
31.3
|
1.0
|
OXT
|
C:ACT404
|
2.3
|
26.5
|
1.0
|
C
|
C:ACT404
|
2.6
|
31.4
|
1.0
|
CG
|
C:ASP177
|
2.7
|
24.8
|
1.0
|
CG
|
C:ASP265
|
2.9
|
28.2
|
1.0
|
OD2
|
C:ASP177
|
2.9
|
26.2
|
1.0
|
CE1
|
C:HIS179
|
3.0
|
25.4
|
1.0
|
CG
|
C:HIS179
|
3.1
|
24.9
|
1.0
|
OD1
|
C:ASP265
|
3.2
|
25.4
|
1.0
|
CB
|
C:HIS179
|
3.5
|
22.7
|
1.0
|
N
|
C:HIS179
|
3.9
|
22.6
|
1.0
|
CA
|
C:GLY302
|
4.0
|
24.6
|
1.0
|
CH3
|
C:ACT404
|
4.1
|
31.6
|
1.0
|
NE2
|
C:HIS179
|
4.1
|
25.8
|
1.0
|
CB
|
C:ASP177
|
4.2
|
22.5
|
1.0
|
NE2
|
C:HIS141
|
4.2
|
26.7
|
1.0
|
CG2
|
C:ILE178
|
4.2
|
26.8
|
1.0
|
CD2
|
C:HIS179
|
4.2
|
26.3
|
1.0
|
CB
|
C:ASP265
|
4.3
|
26.3
|
1.0
|
C17
|
C:YEM406
|
4.3
|
39.7
|
1.0
|
N
|
C:ILE178
|
4.3
|
22.1
|
1.0
|
CA
|
C:HIS179
|
4.4
|
22.2
|
1.0
|
N
|
C:GLY302
|
4.4
|
24.9
|
1.0
|
NE2
|
C:HIS142
|
4.6
|
26.5
|
1.0
|
CE2
|
C:TYR304
|
4.6
|
32.0
|
1.0
|
CE1
|
C:HIS141
|
4.6
|
26.1
|
1.0
|
OH
|
C:TYR304
|
4.7
|
36.9
|
1.0
|
C
|
C:ILE178
|
4.8
|
24.3
|
1.0
|
C
|
C:ASP177
|
4.9
|
25.1
|
1.0
|
CA
|
C:ASP177
|
4.9
|
22.3
|
1.0
|
CA
|
C:ILE178
|
5.0
|
22.4
|
1.0
|
|
Reference:
D.C.Beshore,
G.C.Adam,
R.J.O.Barnard,
C.Burlein,
S.N.Gallicchio,
M.K.Holloway,
D.Krosky,
W.Lemaire,
R.W.Myers,
S.Patel,
M.A.Plotkin,
D.A.Powell,
V.Rada,
C.D.Cox,
P.J.Coleman,
D.J.Klein,
S.E.Wolkenberg.
Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction. Acs Med.Chem.Lett. V. 12 540 2021.
ISSN: ISSN 1948-5875
PubMed: 33854701
DOI: 10.1021/ACSMEDCHEMLETT.1C00074
Page generated: Mon Jul 12 17:23:23 2021
|