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Potassium in PDB 6oda: Crystal Structure of HDAC8 in Complex with Compound 2

Enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 2

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 2:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of HDAC8 in Complex with Compound 2, PDB code: 6oda was solved by X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.750, 91.290, 92.700, 90.00, 94.09, 90.00
R / Rfree (%) 19.9 / 24.9

Other elements in 6oda:

The structure of Crystal Structure of HDAC8 in Complex with Compound 2 also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Zinc (Zn) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of HDAC8 in Complex with Compound 2 (pdb code 6oda). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of HDAC8 in Complex with Compound 2, PDB code: 6oda:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6oda

Go back to Potassium Binding Sites List in 6oda
Potassium binding site 1 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:64.7
occ:1.00
 O A:PHE189 2.7 45.4 1.0
O A:VAL195 2.7 41.3 1.0
O A:TYR225 2.9 40.3 1.0
O A:THR192 3.1 46.4 1.0
C A:PHE189 3.6 45.9 1.0
C A:TYR225 3.6 41.2 1.0
CB A:TYR225 3.9 43.4 1.0
C A:VAL195 3.9 41.2 1.0
OG A:SER226 4.0 39.4 1.0
CB A:PHE189 4.1 43.9 1.0
CA A:SER190 4.3 48.0 1.0
N A:SER226 4.3 40.2 1.0
C A:THR192 4.3 46.7 1.0
N A:SER190 4.3 47.3 1.0
CA A:TYR225 4.4 43.1 1.0
CA A:MET196 4.4 39.9 1.0
C A:SER190 4.5 48.8 1.0
O A:SER190 4.5 49.4 1.0
O A:GLY222 4.5 51.8 1.0
N A:THR197 4.5 38.3 1.0
CA A:PHE189 4.5 44.8 1.0
CG2 A:THR192 4.7 45.7 1.0
N A:MET196 4.7 40.5 1.0
OG1 A:THR197 4.7 38.7 1.0
N A:THR192 4.7 47.8 1.0
CA A:SER226 4.8 38.7 1.0
CG2 A:THR197 4.9 37.5 1.0
C A:MET196 4.9 39.0 1.0
CB A:SER226 5.0 38.8 1.0
CA A:VAL195 5.0 41.9 1.0
CA A:GLY222 5.0 51.5 1.0

Potassium binding site 2 out of 6 in 6oda

Go back to Potassium Binding Sites List in 6oda
Potassium binding site 2 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 2


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 HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:48.9
occ:1.00
 O A:HIS180 2.7 39.8 1.0
O A:ASP178 2.8 40.0 1.0
O A:ASP176 2.8 37.9 1.0
O A:LEU200 2.8 38.8 1.0
OD1 A:ASP176 2.9 39.0 1.0
OG A:SER199 2.9 36.2 1.0
C A:ASP176 3.5 37.1 1.0
CG A:ASP176 3.6 38.3 1.0
C A:LEU200 3.6 38.6 1.0
C A:ASP178 3.7 39.7 1.0
C A:HIS180 3.8 39.7 1.0
N A:ASP178 3.8 39.0 1.0
N A:LEU200 3.9 36.9 1.0
CB A:HIS201 4.0 40.0 1.0
CB A:ASP176 4.0 37.5 1.0
CB A:SER199 4.1 36.4 1.0
C A:LEU177 4.2 38.2 1.0
CA A:ASP178 4.2 39.6 1.0
N A:LEU177 4.2 37.1 1.0
N A:GLY182 4.2 37.0 1.0
ND1 A:HIS201 4.3 40.6 1.0
CA A:HIS181 4.3 38.3 1.0
CA A:LEU177 4.3 37.4 1.0
CB A:ASP178 4.3 40.6 1.0
CA A:SER199 4.3 36.3 1.0
N A:HIS201 4.4 39.3 1.0
CA A:HIS201 4.4 39.7 1.0
CA A:ASP176 4.4 37.1 1.0
N A:HIS181 4.4 39.1 1.0
C A:SER199 4.4 36.8 1.0
CA A:LEU200 4.4 37.8 1.0
OD2 A:ASP176 4.5 38.6 1.0
CG A:HIS201 4.5 40.4 1.0
C A:HIS181 4.5 37.6 1.0
N A:HIS180 4.6 40.3 1.0
C A:LEU179 4.7 40.4 1.0
N A:LEU179 4.8 39.9 1.0
CA A:HIS180 4.8 40.8 1.0
O A:LEU179 4.8 40.9 1.0
CE1 A:HIS142 4.8 37.7 1.0
O A:LEU177 4.9 38.8 1.0

Potassium binding site 3 out of 6 in 6oda

Go back to Potassium Binding Sites List in 6oda
Potassium binding site 3 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:62.4
occ:1.00
 O B:PHE189 2.8 46.8 1.0
O B:VAL195 2.8 46.1 1.0
O B:TYR225 3.0 44.8 1.0
O B:THR192 3.1 53.3 1.0
C B:PHE189 3.7 46.4 1.0
C B:TYR225 3.8 45.5 1.0
OG B:SER226 3.8 43.6 1.0
C B:VAL195 4.0 46.7 1.0
CB B:TYR225 4.1 47.3 1.0
CB B:PHE189 4.2 45.7 1.0
CA B:SER190 4.2 47.4 1.0
C B:THR192 4.3 53.9 1.0
N B:SER190 4.3 47.4 1.0
C B:SER190 4.5 48.7 1.0
CA B:MET196 4.5 44.8 1.0
N B:SER226 4.5 44.4 1.0
O B:GLY222 4.6 55.4 1.0
CA B:TYR225 4.6 46.9 1.0
O B:SER190 4.6 48.7 1.0
CA B:PHE189 4.6 45.9 1.0
CG2 B:THR192 4.7 52.7 1.0
N B:THR197 4.7 43.3 1.0
N B:MET196 4.7 45.6 1.0
N B:THR192 4.8 52.9 1.0
CA B:GLY222 4.8 56.8 1.0
CA B:SER226 4.9 43.0 1.0
CG2 B:THR197 4.9 41.6 1.0
CB B:SER226 4.9 43.0 1.0

Potassium binding site 4 out of 6 in 6oda

Go back to Potassium Binding Sites List in 6oda
Potassium binding site 4 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:36.9
occ:1.00
 O B:ASP178 2.7 43.1 1.0
OD1 B:ASP176 2.7 38.8 1.0
O B:LEU200 2.8 40.2 1.0
O B:HIS180 2.9 42.2 1.0
OG B:SER199 2.9 38.2 1.0
O B:ASP176 2.9 40.5 1.0
C B:ASP176 3.6 40.3 1.0
C B:LEU200 3.6 40.3 1.0
CG B:ASP176 3.7 38.8 1.0
C B:ASP178 3.7 43.0 1.0
N B:ASP178 3.8 42.5 1.0
C B:HIS180 3.8 42.1 1.0
N B:LEU200 3.9 39.7 1.0
CB B:HIS201 4.0 40.3 1.0
ND1 B:HIS201 4.0 40.5 1.0
CB B:ASP176 4.1 39.2 1.0
CB B:SER199 4.1 38.9 1.0
C B:LEU177 4.1 42.3 1.0
CA B:ASP178 4.1 43.0 1.0
N B:LEU177 4.2 40.9 1.0
N B:HIS201 4.3 40.7 1.0
CB B:ASP178 4.3 43.3 1.0
CA B:SER199 4.3 39.6 1.0
CA B:LEU177 4.3 41.6 1.0
CA B:HIS201 4.3 40.6 1.0
C B:SER199 4.3 40.1 1.0
N B:GLY182 4.3 42.2 1.0
CA B:HIS181 4.4 41.5 1.0
CA B:LEU200 4.4 40.1 1.0
CA B:ASP176 4.4 39.9 1.0
CG B:HIS201 4.4 40.4 1.0
N B:HIS181 4.5 41.7 1.0
N B:HIS180 4.5 42.4 1.0
C B:LEU179 4.6 42.4 1.0
C B:HIS181 4.6 41.7 1.0
OD2 B:ASP176 4.7 38.0 1.0
O B:LEU177 4.7 42.5 1.0
N B:LEU179 4.8 42.8 1.0
CA B:HIS180 4.8 42.8 1.0
O B:LEU179 4.8 42.5 1.0

Potassium binding site 5 out of 6 in 6oda

Go back to Potassium Binding Sites List in 6oda
Potassium binding site 5 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:74.2
occ:1.00
 O C:PHE189 2.6 57.2 1.0
O C:VAL195 2.9 54.8 1.0
O C:THR192 3.1 59.6 1.0
O C:TYR225 3.1 70.5 1.0
OG C:SER226 3.5 64.0 1.0
C C:PHE189 3.6 58.5 1.0
C C:TYR225 3.8 70.9 1.0
CB C:TYR225 4.1 72.1 1.0
C C:VAL195 4.1 55.7 1.0
CA C:SER190 4.2 60.2 1.0
CB C:PHE189 4.3 58.6 1.0
C C:THR192 4.3 59.5 1.0
N C:SER226 4.3 69.2 1.0
N C:SER190 4.3 59.1 1.0
OG1 C:THR197 4.4 57.1 1.0
O C:GLY222 4.4 70.8 1.0
O C:SER190 4.4 63.5 1.0
C C:SER190 4.4 62.0 1.0
CA C:TYR225 4.6 72.4 1.0
CA C:PHE189 4.6 58.7 1.0
CB C:SER226 4.6 65.0 1.0
CA C:MET196 4.6 55.8 1.0
CA C:SER226 4.7 66.2 1.0
N C:THR197 4.7 55.2 1.0
N C:THR192 4.7 60.7 1.0
CA C:GLY222 4.8 69.8 1.0
N C:MET196 4.8 55.7 1.0
CG2 C:THR192 4.9 58.9 1.0

Potassium binding site 6 out of 6 in 6oda

Go back to Potassium Binding Sites List in 6oda
Potassium binding site 6 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of HDAC8 in Complex with Compound 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K404

b:53.0
occ:1.00
 O C:ASP176 2.7 52.5 1.0
O C:HIS180 2.7 52.4 1.0
O C:LEU200 2.8 56.1 1.0
O C:ASP178 2.9 52.8 1.0
OD1 C:ASP176 3.0 51.9 1.0
OG C:SER199 3.1 57.0 1.0
C C:ASP176 3.5 52.8 1.0
C C:LEU200 3.7 57.1 1.0
CG C:ASP176 3.7 52.9 1.0
C C:HIS180 3.8 53.9 1.0
C C:ASP178 3.8 52.2 1.0
N C:ASP178 3.9 51.6 1.0
N C:LEU200 3.9 57.0 1.0
CB C:HIS201 4.0 59.0 1.0
CB C:ASP176 4.1 52.8 1.0
ND1 C:HIS201 4.1 58.6 1.0
CA C:ASP178 4.2 51.8 1.0
C C:LEU177 4.2 52.2 1.0
CB C:SER199 4.3 57.4 1.0
N C:LEU177 4.3 52.1 1.0
CB C:ASP178 4.3 52.4 1.0
N C:GLY182 4.3 51.3 1.0
CA C:HIS181 4.3 54.3 1.0
CA C:SER199 4.4 57.3 1.0
CA C:LEU177 4.4 52.3 1.0
N C:HIS201 4.4 58.2 1.0
C C:SER199 4.4 56.9 1.0
CA C:HIS201 4.4 59.0 1.0
CA C:ASP176 4.4 52.9 1.0
CA C:LEU200 4.4 57.6 1.0
N C:HIS181 4.4 55.2 1.0
CG C:HIS201 4.5 59.1 1.0
N C:HIS180 4.6 54.0 1.0
C C:LEU179 4.7 53.4 1.0
OD2 C:ASP176 4.7 53.0 1.0
C C:HIS181 4.7 52.5 1.0
O C:LEU179 4.7 53.3 1.0
CA C:HIS180 4.8 54.9 1.0
N C:LEU179 4.9 52.3 1.0
O C:LEU177 4.9 53.3 1.0

Reference:

X.Zheng, C.Conti, J.Caravella, M.-M.Zablocki, K.Bair, N.Barczak, B.Han, D.Lancia Jr., C.Liu, M.Martin, P.Y.Ng, A.Rudnitskaya, J.J.Thomason, R.Garcia-Dancey, C.Hardy, J.Lahdenranta, C.Leng, P.Li, E.Pardo, A.Saldahna, T.Tan, A.V.Toms, L.Yao, C.Zhang. Structure-Based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-Oxoimidazolidin-1-Yl)Phenyl) Acrylamides As Potent and Selective HDAC8 Inhibitors To Be Published.
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