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Zinc in PDB 6g3o: Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide

Enzymatic activity of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide

All present enzymatic activity of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide, PDB code: 6g3o was solved by T.Isabet, M.Aurelly, L.Chantalat, E.Thoreau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.26 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.050, 93.300, 139.420, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.9

Other elements in 6g3o:

The structure of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Calcium (Ca) 3 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide (pdb code 6g3o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide, PDB code: 6g3o:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6g3o

Go back to Zinc Binding Sites List in 6g3o
Zinc binding site 1 out of 3 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:38.8
occ:1.00
 OD2 A:ASP269 1.9 36.4 1.0
O16 A:EL81004 1.9 35.7 1.0
OD1 A:ASP181 2.1 31.0 1.0
ND1 A:HIS183 2.1 43.2 1.0
O15 A:EL81004 2.4 41.8 1.0
N14 A:EL81004 2.8 35.8 1.0
CG A:ASP269 2.9 36.0 1.0
C13 A:EL81004 2.9 39.4 1.0
CG A:ASP181 3.0 37.1 1.0
CE1 A:HIS183 3.0 42.6 1.0
CG A:HIS183 3.2 41.3 1.0
OD2 A:ASP181 3.2 39.7 1.0
OD1 A:ASP269 3.3 36.1 1.0
CB A:HIS183 3.6 37.3 1.0
N A:HIS183 4.0 36.5 1.0
CA A:GLY306 4.1 35.0 1.0
NE2 A:HIS183 4.2 43.3 1.0
CB A:ASP269 4.2 36.3 1.0
CG2 A:ILE182 4.2 28.6 1.0
NE2 A:HIS145 4.3 38.9 1.0
CD2 A:HIS183 4.3 42.8 1.0
C12 A:EL81004 4.3 41.2 1.0
N A:GLY306 4.3 34.7 1.0
CB A:ASP181 4.4 34.7 1.0
N A:ILE182 4.4 34.2 1.0
CA A:HIS183 4.4 36.6 1.0
OH A:TYR308 4.6 40.1 1.0
CE1 A:HIS145 4.6 38.4 1.0
C11 A:EL81004 4.7 41.0 1.0
CE2 A:TYR308 4.7 37.0 1.0
NE2 A:HIS146 4.8 41.8 1.0
C A:ILE182 4.9 38.4 1.0

Zinc binding site 2 out of 3 in 6g3o

Go back to Zinc Binding Sites List in 6g3o
Zinc binding site 2 out of 3 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:36.3
occ:1.00
 OD2 B:ASP269 1.9 36.6 1.0
O16 B:EL81004 2.0 38.4 1.0
OD1 B:ASP181 2.0 41.1 1.0
ND1 B:HIS183 2.1 38.4 1.0
O15 B:EL81004 2.5 44.5 1.0
N14 B:EL81004 2.7 40.8 1.0
CG B:ASP269 2.9 33.1 1.0
CG B:ASP181 2.9 37.2 1.0
C13 B:EL81004 2.9 42.4 1.0
CE1 B:HIS183 3.0 38.5 1.0
OD2 B:ASP181 3.2 38.1 1.0
CG B:HIS183 3.2 37.1 1.0
OD1 B:ASP269 3.3 38.0 1.0
CB B:HIS183 3.6 33.1 1.0
N B:HIS183 3.9 31.8 1.0
CA B:GLY306 4.0 30.7 1.0
CG2 B:ILE182 4.2 34.0 1.0
CB B:ASP269 4.2 31.3 1.0
NE2 B:HIS183 4.2 39.4 1.0
CD2 B:HIS183 4.3 39.9 1.0
CB B:ASP181 4.3 31.6 1.0
NE2 B:HIS145 4.3 33.3 1.0
N B:ILE182 4.3 30.6 1.0
CA B:HIS183 4.4 32.5 1.0
C12 B:EL81004 4.4 38.6 1.0
N B:GLY306 4.4 30.9 1.0
OH B:TYR308 4.6 36.1 1.0
O B:HOH1200 4.7 52.9 1.0
CE2 B:TYR308 4.7 31.3 1.0
CE1 B:HIS145 4.7 33.2 1.0
C11 B:EL81004 4.8 36.3 1.0
C B:ILE182 4.8 36.2 1.0
NE2 B:HIS146 4.9 37.2 1.0
C B:ASP181 4.9 33.1 1.0
CA B:ILE182 4.9 31.9 1.0

Zinc binding site 3 out of 3 in 6g3o

Go back to Zinc Binding Sites List in 6g3o
Zinc binding site 3 out of 3 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:44.5
occ:1.00
 O16 C:EL81004 1.9 42.1 1.0
OD2 C:ASP269 1.9 44.8 1.0
OD1 C:ASP181 2.0 36.4 1.0
ND1 C:HIS183 2.1 42.0 1.0
O15 C:EL81004 2.4 40.6 1.0
N14 C:EL81004 2.8 42.3 1.0
C13 C:EL81004 2.9 43.0 1.0
CG C:ASP269 2.9 40.2 1.0
CG C:ASP181 2.9 40.0 1.0
CE1 C:HIS183 3.0 42.8 1.0
OD2 C:ASP181 3.2 47.0 1.0
CG C:HIS183 3.2 40.9 1.0
OD1 C:ASP269 3.3 39.2 1.0
CB C:HIS183 3.7 36.9 1.0
N C:HIS183 3.9 38.7 1.0
CA C:GLY306 4.0 37.1 1.0
NE2 C:HIS183 4.2 44.2 1.0
CB C:ASP269 4.2 42.9 1.0
CG2 C:ILE182 4.2 44.8 1.0
NE2 C:HIS145 4.3 40.9 1.0
CD2 C:HIS183 4.3 43.4 1.0
CB C:ASP181 4.3 37.5 1.0
C12 C:EL81004 4.3 43.9 1.0
N C:ILE182 4.4 41.9 1.0
CA C:HIS183 4.4 36.9 1.0
N C:GLY306 4.4 37.4 1.0
OH C:TYR308 4.5 53.4 1.0
CE1 C:HIS145 4.6 40.4 1.0
CE2 C:TYR308 4.7 46.5 1.0
C11 C:EL81004 4.7 46.6 1.0
NE2 C:HIS146 4.8 46.9 1.0
C C:ILE182 4.9 44.8 1.0
C C:ASP181 5.0 45.2 1.0

Reference:

J.F.Fournier, Y.Bhurruth-Alcor, B.Musicki, J.Aubert, M.Aurelly, C.Bouix-Peter, K.Bouquet, L.Chantalat, M.Delorme, B.Drean, G.Duvert, N.Fleury-Bregeot, B.Gauthier, K.Grisendi, C.S.Harris, L.F.Hennequin, T.Isabet, F.Joly, G.Lafitte, C.Millois, R.Morgentin, J.Pascau, D.Piwnica, Y.Rival, C.Soulet, E.Thoreau, L.Tomas. Squaramides As Novel Class I and Iib Histone Deacetylase Inhibitors For Topical Treatment of Cutaneous T-Cell Lymphoma. Bioorg. Med. Chem. Lett. V. 28 2985 2018.
ISSN: ESSN 1464-3405
PubMed: 30122227
DOI: 10.1016/J.BMCL.2018.06.029
Page generated: Mon Oct 28 21:35:53 2024

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