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

Last articles

Ca in 6AHG
Ca in 6AI0
Ca in 6AID
Ca in 6AJ8
Ca in 6AII
Ca in 6A4K
Ca in 5ZZ0
Ca in 6AG0
Ca in 6AGI
Ca in 6A56
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy