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:

Calcium (Ca) 6 atoms

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)


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 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)


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 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)


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 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

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