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Zinc in PDB 7ltl: Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)

Enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19), PDB code: 7ltl 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) 21.77 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.35, 98.76, 139.44, 90, 90, 90
R / Rfree (%) 17 / 19.5

Other elements in 7ltl:

The structure of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19) 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 Lacking A Zinc Binding Group (Compound 19) (pdb code 7ltl). 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 Lacking A Zinc Binding Group (Compound 19), PDB code: 7ltl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7ltl

Go back to Zinc Binding Sites List in 7ltl
Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.8
occ:1.00
 OD2 A:ASP265 1.9 17.8 1.0
OD1 A:ASP177 2.0 16.5 1.0
ND1 A:HIS179 2.0 17.2 1.0
O A:ACT408 2.2 19.6 1.0
OXT A:ACT408 2.3 21.3 1.0
C A:ACT408 2.6 18.6 1.0
CG A:ASP177 2.8 16.8 1.0
CG A:ASP265 2.9 14.9 1.0
CE1 A:HIS179 2.9 17.3 1.0
OD2 A:ASP177 2.9 14.5 1.0
CG A:HIS179 3.2 16.7 1.0
OD1 A:ASP265 3.2 14.7 1.0
CB A:HIS179 3.6 14.9 1.0
N A:HIS179 3.9 14.1 1.0
CA A:GLY302 4.1 16.5 1.0
NE2 A:HIS179 4.1 17.7 1.0
CH3 A:ACT408 4.1 20.6 1.0
CG2 A:ILE178 4.2 16.6 1.0
CB A:ASP177 4.2 15.3 1.0
NE2 A:HIS141 4.2 18.8 1.0
CD2 A:HIS179 4.2 17.2 1.0
CB A:ASP265 4.2 15.4 1.0
C17 A:YEV412 4.3 24.5 1.0
N A:ILE178 4.3 13.8 1.0
N A:GLY302 4.4 16.0 1.0
CA A:HIS179 4.4 14.2 1.0
NE2 A:HIS142 4.5 17.6 1.0
CE2 A:TYR304 4.6 15.0 1.0
OH A:TYR304 4.7 19.7 1.0
CE1 A:HIS141 4.7 18.2 1.0
C A:ILE178 4.9 17.6 1.0
C A:ASP177 4.9 16.6 1.0
CA A:ASP177 4.9 14.2 1.0
CA A:ILE178 5.0 14.4 1.0

Zinc binding site 2 out of 3 in 7ltl

Go back to Zinc Binding Sites List in 7ltl
Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:15.2
occ:1.00
 OD2 B:ASP265 1.9 15.6 1.0
OD1 B:ASP177 2.0 14.9 1.0
ND1 B:HIS179 2.0 14.7 1.0
O B:ACT407 2.3 19.2 1.0
OXT B:ACT407 2.3 20.1 1.0
C B:ACT407 2.6 16.1 1.0
CG B:ASP177 2.8 13.4 1.0
CE1 B:HIS179 2.9 16.1 1.0
CG B:ASP265 2.9 14.1 1.0
OD2 B:ASP177 2.9 13.2 1.0
CG B:HIS179 3.1 14.8 1.0
OD1 B:ASP265 3.2 13.7 1.0
CB B:HIS179 3.6 13.1 1.0
N B:HIS179 3.9 13.6 1.0
CA B:GLY302 4.1 14.4 1.0
NE2 B:HIS179 4.1 16.6 1.0
CG2 B:ILE178 4.1 14.8 1.0
CH3 B:ACT407 4.2 18.2 1.0
CB B:ASP177 4.2 13.2 1.0
CD2 B:HIS179 4.2 16.8 1.0
NE2 B:HIS141 4.3 17.4 1.0
CB B:ASP265 4.3 13.3 1.0
C17 B:YEV410 4.3 26.1 1.0
CA B:HIS179 4.3 12.9 1.0
N B:ILE178 4.4 11.6 1.0
N B:GLY302 4.4 13.2 1.0
CE2 B:TYR304 4.5 13.9 1.0
NE2 B:HIS142 4.6 15.7 1.0
OH B:TYR304 4.6 18.5 1.0
CE1 B:HIS141 4.7 17.4 1.0
C B:ILE178 4.8 16.0 1.0
CA B:ASP177 4.9 12.1 1.0
C B:ASP177 4.9 13.3 1.0

Zinc binding site 3 out of 3 in 7ltl

Go back to Zinc Binding Sites List in 7ltl
Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:20.2
occ:1.00
 OD1 C:ASP177 1.9 20.2 1.0
OD2 C:ASP265 2.0 21.7 1.0
ND1 C:HIS179 2.0 20.3 1.0
OXT C:ACT409 2.2 24.1 1.0
O C:ACT409 2.2 22.8 1.0
C C:ACT409 2.5 22.9 1.0
CG C:ASP177 2.8 20.1 1.0
CG C:ASP265 2.9 20.7 1.0
OD2 C:ASP177 3.0 19.9 1.0
CE1 C:HIS179 3.0 18.9 1.0
CG C:HIS179 3.1 19.2 1.0
OD1 C:ASP265 3.2 19.9 1.0
CB C:HIS179 3.5 18.2 1.0
N C:HIS179 3.8 17.6 1.0
CA C:GLY302 4.0 20.4 1.0
CH3 C:ACT409 4.1 22.1 1.0
NE2 C:HIS179 4.2 19.5 1.0
CG2 C:ILE178 4.2 20.4 1.0
CB C:ASP177 4.2 17.8 1.0
CD2 C:HIS179 4.2 19.6 1.0
C17 C:YEV411 4.2 34.3 1.0
NE2 C:HIS141 4.3 21.5 1.0
CB C:ASP265 4.3 18.5 1.0
CA C:HIS179 4.3 17.9 1.0
N C:ILE178 4.3 17.6 1.0
N C:GLY302 4.4 20.1 1.0
CE2 C:TYR304 4.6 23.1 1.0
NE2 C:HIS142 4.6 20.4 1.0
OH C:TYR304 4.6 25.7 1.0
CE1 C:HIS141 4.7 20.7 1.0
C C:ILE178 4.8 19.6 1.0
C C:ASP177 4.9 19.1 1.0
CA C:ASP177 4.9 17.1 1.0
CA C:ILE178 5.0 17.5 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: Tue Oct 29 23:00:50 2024

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