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Zinc in PDB 4ly1: Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide

Enzymatic activity of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide

All present enzymatic activity of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide:
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide, PDB code: 4ly1 was solved by R.Fong, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.57 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.034, 97.490, 138.922, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.7

Other elements in 4ly1:

The structure of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide (pdb code 4ly1). 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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide, PDB code: 4ly1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ly1

Go back to Zinc Binding Sites List in 4ly1
Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide


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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:13.7
occ:1.00
 N20 A:20Y407 1.9 9.2 0.5
OD2 A:ASP269 1.9 12.2 1.0
OD2 A:ASP181 2.0 14.1 1.0
ND1 A:HIS183 2.0 12.7 1.0
N20 A:20Y407 2.3 16.2 0.5
O12 A:20Y407 2.6 13.3 0.5
O12 A:20Y407 2.6 12.8 0.5
CG A:ASP181 2.8 13.4 1.0
CG A:ASP269 2.9 10.8 1.0
CE1 A:HIS183 2.9 14.0 1.0
C19 A:20Y407 3.0 12.2 0.5
OD1 A:ASP181 3.0 12.6 1.0
CG A:HIS183 3.2 13.6 1.0
C19 A:20Y407 3.2 14.8 0.5
OD1 A:ASP269 3.2 11.0 1.0
C11 A:20Y407 3.3 14.0 0.5
C11 A:20Y407 3.5 13.9 0.5
CB A:HIS183 3.6 12.1 1.0
C14 A:20Y407 3.7 14.0 0.5
C18 A:20Y407 3.8 12.7 0.5
N13 A:20Y407 3.8 14.5 0.5
N A:HIS183 3.9 11.7 1.0
C18 A:20Y407 4.0 12.9 0.5
C14 A:20Y407 4.0 12.8 0.5
N13 A:20Y407 4.1 12.9 0.5
CA A:GLY306 4.1 11.9 1.0
NE2 A:HIS183 4.1 14.1 1.0
NE2 A:HIS145 4.2 13.5 1.0
CG2 A:ILE182 4.2 16.0 1.0
CB A:ASP269 4.2 12.4 1.0
CD2 A:HIS183 4.3 14.1 1.0
CB A:ASP181 4.3 11.4 1.0
N A:GLY306 4.4 12.6 1.0
CA A:HIS183 4.4 11.1 1.0
C8 A:20Y407 4.4 13.2 0.5
NE2 A:HIS146 4.5 13.9 1.0
C8 A:20Y407 4.5 15.4 0.5
N A:ILE182 4.5 10.9 1.0
OH A:TYR308 4.7 14.7 1.0
CE1 A:HIS145 4.7 12.5 1.0
C9 A:20Y407 4.8 17.4 0.5
CE1 A:TYR308 4.8 13.2 1.0
C A:ILE182 5.0 12.5 1.0
C9 A:20Y407 5.0 15.2 0.5

Zinc binding site 2 out of 3 in 4ly1

Go back to Zinc Binding Sites List in 4ly1
Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide


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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:11.6
occ:1.00
 OD1 B:ASP269 2.0 11.1 1.0
OD2 B:ASP181 2.0 10.9 1.0
ND1 B:HIS183 2.0 11.2 1.0
N20 B:20Y408 2.0 10.8 0.5
N20 B:20Y408 2.2 13.4 0.5
O12 B:20Y408 2.6 9.6 0.5
O12 B:20Y408 2.7 11.3 0.5
CG B:ASP181 2.8 12.5 1.0
CE1 B:HIS183 2.9 12.2 1.0
CG B:ASP269 2.9 10.8 1.0
OD1 B:ASP181 3.0 10.1 1.0
C19 B:20Y408 3.0 10.3 0.5
C19 B:20Y408 3.1 11.7 0.5
CG B:HIS183 3.1 11.3 1.0
OD2 B:ASP269 3.3 10.4 1.0
C11 B:20Y408 3.4 13.2 0.5
C11 B:20Y408 3.4 10.6 0.5
CB B:HIS183 3.6 10.4 1.0
C18 B:20Y408 3.8 10.3 0.5
C14 B:20Y408 3.8 11.3 0.5
C14 B:20Y408 3.9 9.9 0.5
N13 B:20Y408 3.9 13.2 0.5
C18 B:20Y408 3.9 10.7 0.5
N B:HIS183 4.0 10.2 1.0
N13 B:20Y408 4.0 10.9 0.5
NE2 B:HIS183 4.1 12.9 1.0
NE2 B:HIS145 4.1 10.8 1.0
CA B:GLY306 4.2 8.5 1.0
CD2 B:HIS183 4.2 13.2 1.0
CB B:ASP181 4.2 8.4 1.0
CG2 B:ILE182 4.3 12.4 1.0
CB B:ASP269 4.3 9.2 1.0
N B:GLY306 4.4 7.9 1.0
CA B:HIS183 4.4 9.3 1.0
NE2 B:HIS146 4.5 11.4 1.0
C8 B:20Y408 4.5 11.8 0.5
C8 B:20Y408 4.5 13.5 0.5
N B:ILE182 4.5 8.7 1.0
CE1 B:HIS145 4.7 10.5 1.0
OH B:TYR308 4.7 11.8 1.0
CE1 B:TYR308 4.8 9.8 1.0
C7 B:20Y408 4.9 12.8 0.5
C B:ILE182 5.0 11.6 1.0

Zinc binding site 3 out of 3 in 4ly1

Go back to Zinc Binding Sites List in 4ly1
Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide


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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:16.6
occ:1.00
 OD2 C:ASP269 2.0 16.2 1.0
N20 C:20Y406 2.0 6.6 0.5
OD2 C:ASP181 2.0 16.3 1.0
ND1 C:HIS183 2.1 17.5 1.0
N20 C:20Y406 2.2 20.8 0.5
O12 C:20Y406 2.5 11.4 0.5
O12 C:20Y406 2.6 26.6 0.5
CG C:ASP181 2.8 14.3 1.0
CG C:ASP269 2.9 18.2 1.0
CE1 C:HIS183 3.0 14.8 1.0
OD1 C:ASP181 3.0 16.5 1.0
C19 C:20Y406 3.1 10.7 0.5
C19 C:20Y406 3.1 20.6 0.5
CG C:HIS183 3.2 15.4 1.0
OD1 C:ASP269 3.3 17.3 1.0
C11 C:20Y406 3.4 10.4 0.5
C11 C:20Y406 3.5 25.2 0.5
CB C:HIS183 3.6 13.8 1.0
C14 C:20Y406 3.8 10.8 0.5
C18 C:20Y406 3.9 20.0 0.5
C18 C:20Y406 3.9 11.8 0.5
C14 C:20Y406 3.9 20.6 0.5
N13 C:20Y406 3.9 8.6 0.5
N C:HIS183 4.0 13.2 1.0
N13 C:20Y406 4.1 20.9 0.5
CA C:GLY306 4.1 13.8 1.0
NE2 C:HIS183 4.2 15.6 1.0
NE2 C:HIS145 4.2 15.8 1.0
CG2 C:ILE182 4.2 16.4 1.0
CD2 C:HIS183 4.3 16.6 1.0
CB C:ASP269 4.3 17.0 1.0
CB C:ASP181 4.3 14.3 1.0
C8 C:20Y406 4.4 10.2 0.5
NE2 C:HIS146 4.4 15.6 1.0
N C:GLY306 4.5 14.8 1.0
CA C:HIS183 4.5 13.1 1.0
N C:ILE182 4.5 14.7 1.0
C8 C:20Y406 4.5 27.6 0.5
CE1 C:HIS145 4.7 14.8 1.0
OH C:TYR308 4.7 18.0 1.0
CE1 C:TYR308 4.9 18.1 1.0
C7 C:20Y406 4.9 11.9 0.5
C C:ILE182 5.0 15.7 1.0

Reference:

B.E.Lauffer, R.Mintzer, R.Fong, S.Mukund, C.Tam, I.Zilberleyb, B.Flicke, A.Ritscher, G.Fedorowicz, R.Vallero, D.F.Ortwine, J.Gunzner, Z.Modrusan, L.Neumann, C.M.Koth, P.J.Lupardus, J.S.Kaminker, C.E.Heise, P.Steiner. Histone Deacetylase (Hdac) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation But Not Transcription and Cell Viability. J.Biol.Chem. V. 288 26926 2013.
ISSN: ISSN 0021-9258
PubMed: 23897821
DOI: 10.1074/JBC.M113.490706
Page generated: Sun Oct 27 02:08:52 2024

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