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Zinc in PDB 6fyz: Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor

Enzymatic activity of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor

All present enzymatic activity of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor:
3.5.1.98;

Protein crystallography data

The structure of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor, PDB code: 6fyz was solved by C.A.Luckhurst, M.C.Maillard, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.70 / 2.15
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 105.530, 105.530, 88.860, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 22.8

Other elements in 6fyz:

The structure of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor (pdb code 6fyz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor, PDB code: 6fyz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6fyz

Go back to Zinc Binding Sites List in 6fyz
Zinc binding site 1 out of 6 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:21.1
occ:1.00
 OD1 A:ASP840 2.0 17.6 1.0
OD2 A:ASP934 2.0 23.4 1.0
O23 A:EBE2001 2.1 26.0 1.0
ND1 A:HIS842 2.1 18.4 1.0
O21 A:EBE2001 2.2 25.0 1.0
CG A:ASP840 2.7 17.5 1.0
N22 A:EBE2001 2.8 26.0 1.0
C20 A:EBE2001 2.8 26.0 1.0
OD2 A:ASP840 2.8 16.2 1.0
CE1 A:HIS842 2.9 18.2 1.0
CG A:ASP934 3.1 23.8 1.0
CG A:HIS842 3.2 17.9 1.0
OD1 A:ASP934 3.4 23.2 1.0
CB A:HIS842 3.6 18.0 1.0
N A:HIS842 3.8 17.6 1.0
NE2 A:HIS842 4.1 18.0 1.0
CB A:ASP840 4.2 17.8 1.0
CA A:GLY974 4.2 23.6 1.0
O A:HOH2153 4.2 27.7 1.0
CD2 A:HIS842 4.2 18.2 1.0
C13 A:EBE2001 4.3 26.1 1.0
NE2 A:HIS802 4.3 17.7 1.0
N A:VAL841 4.3 18.8 1.0
CA A:HIS842 4.3 18.0 1.0
CB A:ASP934 4.4 24.3 1.0
CG1 A:VAL841 4.4 19.7 1.0
C2 A:EBE2001 4.6 27.1 1.0
CE1 A:HIS802 4.6 18.3 1.0
N A:GLY974 4.6 22.5 1.0
C A:VAL841 4.8 18.2 1.0
C A:ASP840 4.8 18.4 1.0
C3 A:EBE2001 4.8 27.0 1.0
CA A:ASP840 4.9 17.9 1.0
NE2 A:HIS803 4.9 17.3 1.0
C14 A:EBE2001 4.9 26.2 1.0
CA A:VAL841 5.0 18.6 1.0
F25 A:EBE2001 5.0 27.6 1.0

Zinc binding site 2 out of 6 in 6fyz

Go back to Zinc Binding Sites List in 6fyz
Zinc binding site 2 out of 6 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:59.0
occ:1.00
 NE2 A:HIS675 2.3 55.6 1.0
SG A:CYS667 2.5 43.4 1.0
SG A:CYS669 2.6 50.5 1.0
CB A:CYS667 3.0 38.9 1.0
CD2 A:HIS675 3.0 55.0 1.0
CE1 A:HIS675 3.4 55.3 1.0
CB A:CYS669 3.6 52.5 1.0
CG A:HIS675 4.2 54.1 1.0
ND1 A:HIS675 4.4 55.7 1.0
CA A:CYS667 4.4 38.5 1.0
N A:CYS669 4.5 51.1 1.0
CA A:CYS669 4.6 54.1 1.0
C A:CYS667 4.8 40.7 1.0
CG2 A:ILE761 5.0 52.4 1.0

Zinc binding site 3 out of 6 in 6fyz

Go back to Zinc Binding Sites List in 6fyz
Zinc binding site 3 out of 6 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:17.1
occ:1.00
 OD2 B:ASP934 2.0 18.6 1.0
OD1 B:ASP840 2.0 14.1 1.0
O23 B:EBE2001 2.1 21.0 1.0
O21 B:EBE2001 2.1 18.7 1.0
CD2 B:HIS842 2.4 13.6 1.0
CG B:ASP840 2.7 14.5 1.0
C20 B:EBE2001 2.8 19.7 1.0
OD2 B:ASP840 2.8 14.1 1.0
N22 B:EBE2001 2.8 20.0 1.0
CG B:ASP934 3.0 18.9 1.0
CG B:HIS842 3.2 13.8 1.0
OD1 B:ASP934 3.5 18.8 1.0
NE2 B:HIS842 3.5 13.4 1.0
CB B:HIS842 3.6 14.4 1.0
N B:HIS842 3.9 14.3 1.0
CB B:ASP840 4.2 14.8 1.0
CA B:GLY974 4.2 18.4 1.0
C13 B:EBE2001 4.2 20.4 1.0
O B:HOH2177 4.3 29.2 1.0
NE2 B:HIS802 4.3 17.2 1.0
CB B:ASP934 4.3 18.0 1.0
N B:VAL841 4.4 14.4 1.0
CA B:HIS842 4.4 14.6 1.0
ND1 B:HIS842 4.4 14.2 1.0
CG1 B:VAL841 4.4 14.9 1.0
CE1 B:HIS842 4.5 13.9 1.0
C4 B:EBE2001 4.5 22.3 1.0
CE1 B:HIS802 4.6 17.1 1.0
N B:GLY974 4.7 17.9 1.0
C3 B:EBE2001 4.8 21.4 1.0
C B:ASP840 4.8 14.7 1.0
NE2 B:HIS803 4.8 15.6 1.0
CA B:ASP840 4.9 14.9 1.0
C B:VAL841 4.9 14.7 1.0
C14 B:EBE2001 4.9 19.6 1.0
N B:GLY975 5.0 19.7 1.0
C B:GLY974 5.0 18.7 1.0

Zinc binding site 4 out of 6 in 6fyz

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Zinc binding site 4 out of 6 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2003

b:39.4
occ:1.00
 NE2 B:HIS675 2.1 41.0 1.0
SG B:CYS669 2.1 34.0 1.0
SG B:CYS751 2.3 51.5 1.0
SG B:CYS667 2.4 30.1 1.0
CE1 B:HIS675 2.9 39.7 1.0
CB B:CYS751 3.1 52.0 1.0
CD2 B:HIS675 3.1 38.6 1.0
CB B:CYS667 3.1 28.8 1.0
CB B:CYS669 3.3 36.8 1.0
ND1 B:HIS675 4.0 39.7 1.0
CG B:HIS675 4.1 38.6 1.0
N B:CYS669 4.3 34.4 1.0
CA B:CYS669 4.3 37.2 1.0
CA B:CYS751 4.5 51.7 1.0
CA B:CYS667 4.5 27.8 1.0
O B:CYS751 4.8 50.1 1.0
C B:CYS751 4.8 50.7 1.0
CA B:GLY753 4.8 46.5 1.0
OG B:SER674 4.8 47.3 1.0
N B:GLY753 4.8 46.5 1.0
C B:CYS667 4.9 28.3 1.0
CD1 B:LEU749 4.9 55.1 1.0

Zinc binding site 5 out of 6 in 6fyz

Go back to Zinc Binding Sites List in 6fyz
Zinc binding site 5 out of 6 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:21.7
occ:1.00
 OD2 C:ASP934 1.9 21.3 1.0
OD1 C:ASP840 2.0 18.3 1.0
O23 C:EBE2001 2.0 20.3 1.0
ND1 C:HIS842 2.1 19.9 1.0
O21 C:EBE2001 2.2 22.7 1.0
CG C:ASP840 2.8 20.1 1.0
N22 C:EBE2001 2.8 22.5 1.0
C20 C:EBE2001 2.8 22.9 1.0
OD2 C:ASP840 2.8 20.3 1.0
CE1 C:HIS842 2.9 20.1 1.0
CG C:ASP934 3.0 22.1 1.0
CG C:HIS842 3.2 19.2 1.0
OD1 C:ASP934 3.4 22.4 1.0
CB C:HIS842 3.6 19.4 1.0
N C:HIS842 4.0 19.1 1.0
NE2 C:HIS842 4.1 20.2 1.0
O C:HOH2131 4.1 31.4 1.0
CD2 C:HIS842 4.2 19.1 1.0
CB C:ASP840 4.2 19.7 1.0
NE2 C:HIS802 4.3 20.4 1.0
C13 C:EBE2001 4.3 23.4 1.0
CA C:GLY974 4.3 20.3 1.0
CB C:ASP934 4.3 21.3 1.0
CA C:HIS842 4.4 19.6 1.0
N C:VAL841 4.4 19.5 1.0
CG1 C:VAL841 4.5 21.3 1.0
CE1 C:HIS802 4.6 20.7 1.0
C4 C:EBE2001 4.6 24.2 1.0
N C:GLY974 4.7 20.0 1.0
NE2 C:HIS803 4.7 22.2 1.0
C3 C:EBE2001 4.8 23.9 1.0
C C:ASP840 4.9 19.1 1.0
C C:VAL841 4.9 20.5 1.0
C14 C:EBE2001 4.9 22.9 1.0
CA C:ASP840 4.9 20.0 1.0
O C:LEU943 5.0 30.2 1.0

Zinc binding site 6 out of 6 in 6fyz

Go back to Zinc Binding Sites List in 6fyz
Zinc binding site 6 out of 6 in the Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:57.0
occ:1.00
 NE2 C:HIS675 2.3 51.5 1.0
SG C:CYS667 2.4 42.9 1.0
SG C:CYS669 3.1 64.2 1.0
CE1 C:HIS675 3.1 51.7 1.0
CB C:CYS669 3.3 54.0 1.0
CB C:CYS667 3.3 38.4 1.0
CD2 C:HIS675 3.3 51.0 1.0
ND1 C:HIS675 4.3 52.6 1.0
N C:CYS669 4.3 48.1 1.0
CA C:CYS669 4.4 51.2 1.0
CG C:HIS675 4.4 50.6 1.0
CA C:CYS667 4.7 36.2 1.0
C C:CYS667 4.9 37.9 1.0
CG2 C:ILE761 5.0 51.7 1.0

Reference:

C.A.Luckhurst, O.Aziz, V.Beaumont, R.W.Burli, P.Breccia, M.C.Maillard, A.F.Haughan, M.Lamers, P.Leonard, K.L.Matthews, G.Raphy, A.J.Stott, I.Munoz-Sanjuan, B.Thomas, M.Wall, G.Wishart, D.Yates, C.Dominguez. Development and Characterization of A Cns-Penetrant Benzhydryl Hydroxamic Acid Class Iia Histone Deacetylase Inhibitor. Bioorg. Med. Chem. Lett. V. 29 83 2019.
ISSN: ESSN 1464-3405
PubMed: 30463802
DOI: 10.1016/J.BMCL.2018.11.009
Page generated: Mon Oct 28 21:29:42 2024

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