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Zinc in PDB 4cby: Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease

Enzymatic activity of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease

All present enzymatic activity of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease:
3.5.1.98;

Protein crystallography data

The structure of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease, PDB code: 4cby was solved by R.W.Burli, C.A.Luckhurst, O.Aziz, K.L.Matthews, D.Yates, K.A.Lyons, M.Beconi, G.Mcallister, P.Breccia, A.J.Stott, S.D.Penrose, M.Wall, M.Lamers, P.Leonard, I.Mueller, C.M.Richardson, R.Jarvis, L.Stones, S.Hughes, G.Wishart, A.F.Haughan, C.Oconnell, T.Mead, H.Mcneil, J.Vann, J.Mangette, M.Maillard, V.Beaumont, I.Munoz-Sanjuan, C.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.1 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.151, 161.816, 83.732, 90.00, 97.03, 90.00
R / Rfree (%) 20.907 / 24.592

Other elements in 4cby:

The structure of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease (pdb code 4cby). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease, PDB code: 4cby:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4cby

Go back to Zinc Binding Sites List in 4cby
Zinc binding site 1 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2034

b:19.7
occ:1.00
OD2 A:ASP934 2.0 23.4 1.0
O22 A:KEE2033 2.0 24.9 1.0
OD1 A:ASP840 2.0 18.5 1.0
ND1 A:HIS842 2.1 21.8 1.0
O24 A:KEE2033 2.2 26.9 1.0
OD2 A:ASP840 2.6 18.3 1.0
C1 A:KEE2033 2.6 27.8 1.0
CG A:ASP840 2.6 19.3 1.0
N23 A:KEE2033 2.7 27.9 1.0
CG A:ASP934 2.9 26.0 1.0
CE1 A:HIS842 3.0 22.7 1.0
CG A:HIS842 3.2 22.2 1.0
OD1 A:ASP934 3.3 25.9 1.0
CB A:HIS842 3.5 22.3 1.0
N A:HIS842 3.8 21.6 1.0
CG1 A:VAL841 4.0 22.4 1.0
C2 A:KEE2033 4.1 28.3 1.0
O A:HOH2021 4.1 30.0 1.0
CB A:ASP840 4.1 19.9 1.0
CA A:GLY974 4.1 29.2 1.0
NE2 A:HIS842 4.2 23.7 1.0
CB A:ASP934 4.2 25.8 1.0
CA A:HIS842 4.3 22.2 1.0
CD2 A:HIS842 4.3 22.8 1.0
N A:VAL841 4.4 20.7 1.0
NE2 A:HIS802 4.4 24.4 1.0
N A:GLY974 4.6 29.3 1.0
C A:VAL841 4.8 21.5 1.0
CE1 A:HIS802 4.8 25.1 1.0
C A:ASP840 4.8 20.6 1.0
CA A:ASP840 4.9 20.2 1.0
NE2 A:HIS803 4.9 22.1 1.0
CA A:VAL841 4.9 21.4 1.0
C3 A:KEE2033 5.0 29.3 1.0
C A:GLY974 5.0 30.3 1.0

Zinc binding site 2 out of 8 in 4cby

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Zinc binding site 2 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2035

b:25.4
occ:1.00
NE2 A:HIS675 2.1 27.0 1.0
SG A:CYS669 2.2 27.7 1.0
SG A:CYS667 2.3 24.8 1.0
SG A:CYS751 2.3 25.9 1.0
CD2 A:HIS675 3.0 28.4 1.0
CE1 A:HIS675 3.1 26.9 1.0
CB A:CYS667 3.2 25.7 1.0
CB A:CYS669 3.3 28.8 1.0
CB A:CYS751 3.4 26.7 1.0
CG A:HIS675 4.2 29.4 1.0
ND1 A:HIS675 4.2 27.2 1.0
N A:CYS669 4.2 28.3 1.0
CA A:CYS669 4.3 28.8 1.0
N A:GLY753 4.5 32.6 1.0
CA A:CYS667 4.5 25.8 1.0
CA A:GLY753 4.6 33.1 1.0
CA A:CYS751 4.6 28.1 1.0
O A:CYS751 4.7 29.5 1.0
C A:CYS751 4.7 28.9 1.0
O A:SER671 4.7 35.1 1.0
CB A:SER674 4.7 43.0 1.0
C A:CYS667 4.8 26.4 1.0
CD1 A:LEU749 5.0 28.6 1.0

Zinc binding site 3 out of 8 in 4cby

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Zinc binding site 3 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2033

b:23.5
occ:1.00
O22 B:KEE2032 2.0 23.4 1.0
OD2 B:ASP934 2.0 22.6 1.0
OD1 B:ASP840 2.0 20.2 1.0
ND1 B:HIS842 2.1 21.0 1.0
O24 B:KEE2032 2.2 23.6 1.0
OD2 B:ASP840 2.6 19.1 1.0
C1 B:KEE2032 2.6 24.9 1.0
CG B:ASP840 2.7 19.8 1.0
N23 B:KEE2032 2.7 24.2 1.0
CE1 B:HIS842 3.0 21.3 1.0
CG B:ASP934 3.0 22.1 1.0
CG B:HIS842 3.1 20.7 1.0
OD1 B:ASP934 3.4 21.3 1.0
CB B:HIS842 3.5 21.2 1.0
N B:HIS842 3.8 21.2 1.0
O B:HOH2017 4.0 16.7 1.0
CG1 B:VAL841 4.0 21.3 1.0
C2 B:KEE2032 4.0 25.9 1.0
NE2 B:HIS842 4.1 21.6 1.0
CB B:ASP840 4.2 20.5 1.0
CA B:GLY974 4.2 23.5 1.0
CD2 B:HIS842 4.2 21.5 1.0
CA B:HIS842 4.2 21.3 1.0
CB B:ASP934 4.3 21.8 1.0
NE2 B:HIS802 4.4 18.5 1.0
N B:VAL841 4.4 21.1 1.0
N B:GLY974 4.6 22.9 1.0
C3 B:KEE2032 4.7 27.2 1.0
CE1 B:HIS802 4.8 18.4 1.0
C B:VAL841 4.8 21.0 1.0
C B:ASP840 4.9 20.7 1.0
NE2 B:HIS803 4.9 27.5 1.0
CA B:ASP840 5.0 20.6 1.0
CA B:VAL841 5.0 21.0 1.0

Zinc binding site 4 out of 8 in 4cby

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Zinc binding site 4 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2034

b:28.3
occ:1.00
NE2 B:HIS675 2.1 28.0 1.0
SG B:CYS751 2.3 31.9 1.0
SG B:CYS669 2.3 27.6 1.0
SG B:CYS667 2.3 27.8 1.0
CD2 B:HIS675 3.1 27.9 1.0
CE1 B:HIS675 3.1 27.7 1.0
CB B:CYS667 3.2 27.5 1.0
CB B:CYS669 3.3 28.5 1.0
CB B:CYS751 3.3 32.8 1.0
ND1 B:HIS675 4.2 27.8 1.0
CG B:HIS675 4.2 27.4 1.0
N B:CYS669 4.3 28.2 1.0
CA B:CYS669 4.4 28.5 1.0
N B:GLY753 4.4 37.7 1.0
CA B:GLY753 4.5 36.9 1.0
CA B:CYS667 4.6 27.5 1.0
CA B:CYS751 4.6 33.1 1.0
O B:CYS751 4.7 34.9 1.0
C B:CYS751 4.7 33.8 1.0
CB B:SER674 4.8 31.7 1.0
C B:CYS667 4.8 28.9 1.0
O B:SER671 4.9 26.6 1.0
N B:THR668 5.0 29.3 1.0

Zinc binding site 5 out of 8 in 4cby

Go back to Zinc Binding Sites List in 4cby
Zinc binding site 5 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2034

b:25.9
occ:1.00
O22 C:KEE2033 2.0 26.9 1.0
OD2 C:ASP934 2.0 24.5 1.0
OD1 C:ASP840 2.0 23.5 1.0
ND1 C:HIS842 2.1 22.5 1.0
O24 C:KEE2033 2.2 26.6 1.0
C1 C:KEE2033 2.6 27.6 1.0
OD2 C:ASP840 2.6 23.5 1.0
N23 C:KEE2033 2.6 27.0 1.0
CG C:ASP840 2.7 23.0 1.0
CE1 C:HIS842 3.0 22.8 1.0
CG C:ASP934 3.0 23.4 1.0
CG C:HIS842 3.1 21.8 1.0
OD1 C:ASP934 3.4 22.4 1.0
CB C:HIS842 3.5 21.2 1.0
N C:HIS842 3.8 20.3 1.0
C2 C:KEE2033 4.0 29.2 1.0
CG1 C:VAL841 4.1 21.4 1.0
CA C:GLY974 4.2 25.8 1.0
CB C:ASP840 4.2 22.9 1.0
NE2 C:HIS842 4.2 22.1 1.0
CD2 C:HIS842 4.3 22.6 1.0
CA C:HIS842 4.3 21.0 1.0
CB C:ASP934 4.3 23.8 1.0
NE2 C:HIS802 4.3 29.6 1.0
N C:VAL841 4.5 21.3 1.0
N C:GLY974 4.6 26.1 1.0
O C:HOH2019 4.6 32.3 1.0
CE1 C:HIS802 4.7 30.8 1.0
C3 C:KEE2033 4.8 29.9 1.0
NE2 C:HIS803 4.8 27.6 1.0
C C:VAL841 4.8 19.9 1.0
C C:ASP840 4.9 22.2 1.0
CA C:ASP840 5.0 22.4 1.0

Zinc binding site 6 out of 8 in 4cby

Go back to Zinc Binding Sites List in 4cby
Zinc binding site 6 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2035

b:46.8
occ:1.00
NE2 C:HIS675 2.2 49.6 1.0
SG C:CYS667 2.3 42.9 1.0
SG C:CYS751 2.3 46.5 1.0
SG C:CYS669 2.4 56.6 1.0
CE1 C:HIS675 3.1 47.6 1.0
CB C:CYS751 3.2 50.7 1.0
CD2 C:HIS675 3.2 47.7 1.0
CB C:CYS667 3.2 44.5 1.0
CB C:CYS669 3.4 58.0 1.0
N C:CYS669 4.3 64.0 1.0
ND1 C:HIS675 4.3 46.2 1.0
CG C:HIS675 4.3 46.8 1.0
CA C:CYS669 4.4 62.3 1.0
CA C:CYS751 4.5 52.8 1.0
CA C:CYS667 4.6 44.4 1.0
O C:CYS751 4.7 48.2 1.0
C C:CYS751 4.7 50.8 1.0
N C:GLY753 4.8 51.3 1.0
C C:CYS667 4.9 46.7 1.0
CD1 C:LEU749 4.9 58.3 1.0
CA C:GLY753 5.0 46.8 1.0
O C:SER671 5.0 79.5 1.0
N C:THR668 5.0 54.1 1.0

Zinc binding site 7 out of 8 in 4cby

Go back to Zinc Binding Sites List in 4cby
Zinc binding site 7 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2037

b:25.3
occ:1.00
O22 D:KEE2036 2.0 29.9 1.0
OD2 D:ASP934 2.0 22.9 1.0
OD1 D:ASP840 2.0 22.9 1.0
ND1 D:HIS842 2.1 24.1 1.0
O24 D:KEE2036 2.2 28.9 1.0
OD2 D:ASP840 2.6 21.2 1.0
C1 D:KEE2036 2.6 32.0 1.0
CG D:ASP840 2.6 21.5 1.0
N23 D:KEE2036 2.7 31.5 1.0
CE1 D:HIS842 3.0 24.9 1.0
CG D:ASP934 3.0 22.0 1.0
CG D:HIS842 3.1 24.2 1.0
OD1 D:ASP934 3.4 20.9 1.0
CB D:HIS842 3.5 23.9 1.0
N D:HIS842 3.8 22.8 1.0
C2 D:KEE2036 4.0 32.6 1.0
CA D:GLY974 4.1 30.5 1.0
O D:HOH2016 4.1 37.4 1.0
CB D:ASP840 4.2 21.2 1.0
NE2 D:HIS842 4.2 25.5 1.0
CG1 D:VAL841 4.3 21.1 1.0
CD2 D:HIS842 4.3 25.6 1.0
CA D:HIS842 4.3 23.9 1.0
CB D:ASP934 4.3 21.7 1.0
NE2 D:HIS802 4.4 24.3 1.0
N D:VAL841 4.5 21.8 1.0
N D:GLY974 4.6 30.4 1.0
C3 D:KEE2036 4.7 34.5 1.0
CE1 D:HIS802 4.8 24.4 1.0
C D:VAL841 4.8 22.1 1.0
NE2 D:HIS803 4.9 33.2 1.0
C D:ASP840 4.9 21.3 1.0
CA D:ASP840 5.0 20.9 1.0
C D:GLY974 5.0 33.2 1.0

Zinc binding site 8 out of 8 in 4cby

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Zinc binding site 8 out of 8 in the Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Hdac Inhibitors As A Potential Therapy For Huntingtons Disease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2038

b:45.7
occ:1.00
NE2 D:HIS675 2.2 50.7 1.0
SG D:CYS667 2.3 42.2 1.0
SG D:CYS751 2.3 51.4 1.0
SG D:CYS669 2.3 49.6 1.0
CE1 D:HIS675 3.1 51.9 1.0
CB D:CYS751 3.2 54.8 1.0
CD2 D:HIS675 3.2 51.2 1.0
CB D:CYS667 3.2 41.6 1.0
CB D:CYS669 3.3 51.6 1.0
N D:CYS669 4.2 52.2 1.0
ND1 D:HIS675 4.3 53.0 1.0
CG D:HIS675 4.3 52.5 1.0
CA D:CYS669 4.4 53.7 1.0
CA D:CYS751 4.5 54.7 1.0
CA D:CYS667 4.6 41.4 1.0
O D:CYS751 4.7 53.5 1.0
C D:CYS751 4.7 52.6 1.0
N D:GLY753 4.8 52.0 1.0
C D:CYS667 4.8 42.4 1.0
CD1 D:LEU749 4.9 45.8 1.0
O D:SER671 4.9 76.1 1.0
N D:THR668 5.0 44.9 1.0

Reference:

R.W.Burli, C.A.Luckhurst, O.Aziz, K.L.Matthews, D.Yates, K.A.Lyons, M.Beconi, G.Mcallister, P.Breccia, A.J.Stott, S.D.Penrose, M.Wall, M.B.A.C.Lamers, P.Leonard, I.Mueller, C.M.Richardson, R.Jarvis, L.Stones, S.Hughes, G.Wishart, A.F.Haughan, C.O'connell, T.Mead, H.Mcneil, J.Vann, J.Mangette, M.Maillard, V.Beaumont, I.Munoz-Sanjuan, C.Dominguez. Design, Synthesis, and Biological Evaluation of Potent and Selective Class Iia Histone Deacetylase (Hdac) Inhibitors As A Potential Therapy For Huntington'S Disease. J.Med.Chem. V. 56 9934 2013.
ISSN: ISSN 0022-2623
PubMed: 24261862
DOI: 10.1021/JM4011884
Page generated: Wed Dec 16 05:08:22 2020

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