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Potassium in PDB 7u6b: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor, PDB code: 7u6b was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.71 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.499, 80.499, 247.678, 90, 90, 120
R / Rfree (%) 18.5 / 23.2

Other elements in 7u6b:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor (pdb code 7u6b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor, PDB code: 7u6b:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7u6b

Go back to Potassium Binding Sites List in 7u6b
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K702

b:31.5
occ:1.00
 O B:TRP196 2.6 35.9 1.0
O B:HIS176 2.6 27.6 1.0
O B:ASP174 2.7 36.5 1.0
O B:ASP172 2.8 29.4 1.0
OD2 B:ASP172 2.9 32.2 1.0
OG B:SER195 3.0 31.9 1.0
CG B:ASP172 3.2 32.6 1.0
C B:ASP174 3.5 35.0 1.0
C B:ASP172 3.6 34.3 1.0
C B:HIS176 3.7 34.0 1.0
OD1 B:ASP172 3.7 36.6 1.0
N B:ASP174 3.8 31.9 1.0
C B:TRP196 3.8 35.6 1.0
CB B:ASP172 3.9 30.4 1.0
CB B:SER195 4.0 33.6 1.0
CA B:ASP174 4.0 33.0 1.0
CB B:ASP174 4.0 30.5 1.0
N B:TRP196 4.2 30.9 1.0
N B:HIS176 4.3 32.5 1.0
C B:TRP173 4.3 31.8 1.0
CA B:SER195 4.3 32.6 1.0
CB B:HIS197 4.3 31.4 1.0
N B:TRP173 4.4 36.7 1.0
CA B:ASP172 4.4 29.2 1.0
CA B:HIS177 4.4 34.3 1.0
N B:GLY178 4.4 32.5 1.0
N B:HIS177 4.4 33.5 1.0
ND1 B:HIS197 4.5 38.0 1.0
CA B:TRP173 4.5 30.9 1.0
N B:VAL175 4.5 37.8 1.0
C B:SER195 4.5 37.1 1.0
CA B:HIS176 4.6 30.7 1.0
C B:VAL175 4.6 37.7 1.0
CA B:TRP196 4.7 33.8 1.0
CE1 B:HIS136 4.7 38.1 1.0
CD1 B:TRP196 4.7 32.2 1.0
CA B:HIS197 4.7 33.1 1.0
C B:HIS177 4.8 35.0 1.0
N B:HIS197 4.8 30.1 1.0
OH B:TYR193 4.8 29.6 1.0
ND1 B:HIS136 4.9 30.4 1.0
CA B:VAL175 4.9 37.9 1.0
CG B:HIS197 4.9 37.2 1.0
OD2 B:ASP174 5.0 38.8 1.0

Potassium binding site 2 out of 2 in 7u6b

Go back to Potassium Binding Sites List in 7u6b
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Indolethyl Piperidine-4-Acrylhydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K703

b:55.9
occ:1.00
 O B:HOH804 2.5 44.8 1.0
O B:PHE185 2.5 37.2 1.0
O B:VAL191 2.6 41.6 1.0
O B:ASP188 2.9 41.0 1.0
O B:PHE224 3.1 37.6 1.0
O B:HOH844 3.3 36.8 1.0
C B:PHE185 3.6 37.4 1.0
CB B:PHE224 3.6 38.2 1.0
C B:PHE224 3.7 38.9 1.0
C B:VAL191 3.8 39.2 1.0
CB B:PHE185 3.8 32.0 1.0
C B:ASP188 3.9 47.5 1.0
CA B:PHE224 4.3 38.7 1.0
N B:ASP188 4.3 43.9 1.0
CA B:PHE185 4.3 36.4 1.0
N B:ASN225 4.4 37.6 1.0
CA B:GLU186 4.4 43.1 1.0
N B:GLU186 4.5 33.9 1.0
CA B:ASP188 4.5 46.9 1.0
O B:GLU186 4.5 39.0 1.0
C B:GLU186 4.6 43.9 1.0
O B:GLY221 4.6 44.3 1.0
CA B:VAL191 4.7 39.6 1.0
N B:LEU192 4.7 37.1 1.0
CA B:LEU192 4.7 40.8 1.0
N B:TYR193 4.7 30.9 1.0
CB B:VAL191 4.7 39.4 1.0
CB B:ASP188 4.8 41.8 1.0
N B:PRO189 4.8 41.3 1.0
N B:VAL191 4.8 34.2 1.0
CG B:PHE224 4.9 38.3 1.0
CA B:ASN225 5.0 36.3 1.0
CA B:PRO189 5.0 34.1 1.0

Reference:

P.Zeyen, Y.Zeyn, D.Herp, F.Mahmoudi, T.Z.Yesiloglu, F.Erdmann, M.Schmidt, D.Robaa, C.Romier, J.Ridinger, C.J.Herbst-Gervasoni, D.W.Christianson, I.Oehme, M.Jung, O.H.Kramer, W.Sippl. Identification of Histone Deacetylase 10 (HDAC10) Inhibitors That Modulate Autophagy in Transformed Cells. Eur.J.Med.Chem. V. 234 14272 2022.
ISSN: ISSN 0223-5234
PubMed: 35306288
DOI: 10.1016/J.EJMECH.2022.114272
Page generated: Mon Aug 12 21:19:23 2024

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