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Zinc in PDB 5a2s: Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors

Enzymatic activity of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors

All present enzymatic activity of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors:
3.5.1.98;

Protein crystallography data

The structure of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors, PDB code: 5a2s was solved by C.A.Luckhurst, P.Breccia, A.J.Stott, O.Aziz, H.Birch, R.W.Burli, S.Hughes, R.E.Jarvis, M.Lamers, P.Leonard, K.L.Matthews, G.Mcallister, S.Pollack, E.Saville-Stones, G.Wishart, D.Yates, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 161.63 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.948, 82.141, 161.626, 90.00, 90.00, 90.00
R / Rfree (%) 18.523 / 25.647

Other elements in 5a2s:

The structure of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors (pdb code 5a2s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors, PDB code: 5a2s:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5a2s

Go back to Zinc Binding Sites List in 5a2s
Zinc binding site 1 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:20.1
occ:1.00
 O6 A:OTF1 2.0 21.7 1.0
OD2 A:ASP934 2.0 20.2 1.0
OD1 A:ASP840 2.0 18.7 1.0
ND1 A:HIS842 2.1 19.1 1.0
O8 A:OTF1 2.2 22.1 1.0
OD2 A:ASP840 2.6 19.0 1.0
C1 A:OTF1 2.6 22.5 1.0
CG A:ASP840 2.6 18.5 1.0
N7 A:OTF1 2.7 22.6 1.0
CE1 A:HIS842 3.0 19.4 1.0
CG A:ASP934 3.0 20.1 1.0
CG A:HIS842 3.2 18.9 1.0
OD1 A:ASP934 3.3 19.7 1.0
CB A:HIS842 3.6 18.9 1.0
N A:HIS842 3.9 18.5 1.0
CA A:GLY974 4.0 23.1 1.0
C2 A:OTF1 4.1 22.8 1.0
CG1 A:VAL841 4.1 18.2 1.0
CB A:ASP840 4.2 18.5 1.0
NE2 A:HIS842 4.2 19.3 1.0
O A:HOH2001 4.3 24.3 1.0
N A:VAL841 4.3 18.6 1.0
CD2 A:HIS842 4.3 19.2 1.0
CB A:ASP934 4.3 20.2 1.0
NE2 A:HIS802 4.4 21.7 1.0
CA A:HIS842 4.4 18.6 1.0
N A:GLY974 4.5 22.1 1.0
CE1 A:HIS802 4.7 21.1 1.0
F5 A:OTF1 4.8 22.8 1.0
C3 A:OTF1 4.8 23.5 1.0
C A:GLY974 4.8 24.4 1.0
C A:VAL841 4.9 18.4 1.0
C A:ASP840 4.9 18.7 1.0
NE2 A:HIS803 4.9 21.4 1.0
CA A:ASP840 4.9 18.4 1.0
CA A:VAL841 4.9 18.4 1.0
CB A:VAL841 5.0 18.4 1.0

Zinc binding site 2 out of 4 in 5a2s

Go back to Zinc Binding Sites List in 5a2s
Zinc binding site 2 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:27.8
occ:1.00
 NE2 A:HIS675 2.1 27.6 1.0
SG A:CYS669 2.3 28.2 1.0
SG A:CYS751 2.3 32.6 1.0
SG A:CYS667 2.3 25.7 1.0
CE1 A:HIS675 3.1 28.3 1.0
CD2 A:HIS675 3.1 27.6 1.0
CB A:CYS667 3.2 26.5 1.0
CB A:CYS669 3.2 28.2 1.0
CB A:CYS751 3.3 31.6 1.0
ND1 A:HIS675 4.3 28.8 1.0
CG A:HIS675 4.3 28.1 1.0
N A:CYS669 4.3 28.7 1.0
CB A:SER674 4.3 33.1 1.0
CA A:CYS669 4.4 28.3 1.0
N A:GLY753 4.4 27.2 1.0
CA A:GLY753 4.5 26.5 1.0
CA A:CYS751 4.6 31.4 1.0
CA A:CYS667 4.6 26.6 1.0
O A:SER671 4.7 31.6 1.0
C A:CYS751 4.7 31.0 1.0
O A:CYS751 4.8 32.4 1.0
OG A:SER674 4.8 33.9 1.0
C A:CYS667 4.9 27.1 1.0

Zinc binding site 3 out of 4 in 5a2s

Go back to Zinc Binding Sites List in 5a2s
Zinc binding site 3 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:22.4
occ:1.00
 O6 B:OTF1 2.0 25.7 1.0
OD1 B:ASP840 2.0 20.8 1.0
OD2 B:ASP934 2.0 22.2 1.0
ND1 B:HIS842 2.1 20.4 1.0
O8 B:OTF1 2.2 23.9 1.0
OD2 B:ASP840 2.6 20.4 1.0
CG B:ASP840 2.6 20.9 1.0
C1 B:OTF1 2.7 26.2 1.0
N7 B:OTF1 2.8 25.0 1.0
CE1 B:HIS842 2.9 20.6 1.0
CG B:ASP934 3.0 22.7 1.0
CG B:HIS842 3.2 20.6 1.0
OD1 B:ASP934 3.4 22.0 1.0
CB B:HIS842 3.7 20.8 1.0
N B:HIS842 3.9 20.8 1.0
CG1 B:VAL841 4.0 20.4 1.0
O B:HOH2001 4.0 23.0 1.0
C2 B:OTF1 4.1 27.9 1.0
NE2 B:HIS842 4.1 20.8 1.0
CB B:ASP840 4.1 20.2 1.0
CA B:GLY974 4.1 24.6 1.0
CD2 B:HIS842 4.3 21.1 1.0
N B:VAL841 4.3 20.2 1.0
CB B:ASP934 4.4 22.9 1.0
NE2 B:HIS802 4.4 19.8 1.0
CA B:HIS842 4.4 20.9 1.0
N B:GLY974 4.6 24.5 1.0
CE1 B:HIS802 4.7 19.9 1.0
F5 B:OTF1 4.7 28.5 1.0
C B:VAL841 4.8 20.7 1.0
C B:ASP840 4.8 20.1 1.0
N B:GLY975 4.8 24.9 1.0
C3 B:OTF1 4.9 28.4 1.0
CA B:ASP840 4.9 19.9 1.0
C B:GLY974 4.9 24.6 1.0
NE2 B:HIS803 4.9 23.3 1.0
CA B:VAL841 4.9 20.4 1.0

Zinc binding site 4 out of 4 in 5a2s

Go back to Zinc Binding Sites List in 5a2s
Zinc binding site 4 out of 4 in the Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Potent, Selective and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:34.5
occ:1.00
 NE2 B:HIS675 2.1 35.6 1.0
SG B:CYS751 2.3 39.1 1.0
SG B:CYS669 2.3 35.5 1.0
SG B:CYS667 2.3 33.4 1.0
CD2 B:HIS675 2.9 35.4 1.0
CB B:CYS667 3.2 33.1 1.0
CE1 B:HIS675 3.3 35.2 1.0
CB B:CYS669 3.3 34.8 1.0
CB B:CYS751 3.5 40.1 1.0
CG B:HIS675 4.2 35.4 1.0
N B:CYS669 4.3 36.0 1.0
OG B:SER674 4.3 43.5 1.0
ND1 B:HIS675 4.3 35.0 1.0
CA B:CYS669 4.4 35.2 1.0
CA B:CYS667 4.6 32.8 1.0
CG2 B:ILE761 4.7 34.8 1.0
CA B:CYS751 4.8 41.1 1.0
CD1 B:LEU749 4.9 46.2 1.0
O B:CYS751 4.9 41.0 1.0
C B:CYS667 4.9 33.1 1.0
CA B:GLY753 4.9 41.9 1.0
C B:CYS751 5.0 41.3 1.0
C B:CYS669 5.0 34.4 1.0

Reference:

C.A.Luckhurst, P.Breccia, A.J.Stott, O.Aziz, H.L.Birch, R.W.Burli, S.J.Hughes, R.E.Jarvis, M.Lamers, P.M.Leonard, K.L.Matthews, G.Mcallister, S.Pollack, E.Saville-Stones, G.Wishart, D.Yates, C.Dominguez. Potent, Selective, and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors. Acs Med.Chem.Lett. V. 7 34 2016.
ISSN: ISSN 1948-5875
PubMed: 26819662
DOI: 10.1021/ACSMEDCHEMLETT.5B00302
Page generated: Sun Oct 27 12:35:34 2024

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