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Potassium in PDB 6odb: Crystal Structure of HDAC8 in Complex with Compound 3

Enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 3

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 3:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of HDAC8 in Complex with Compound 3, PDB code: 6odb 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.915, 90.950, 93.067, 90.00, 94.10, 90.00
R / Rfree (%) 19.5 / 24.1

Other elements in 6odb:

The structure of Crystal Structure of HDAC8 in Complex with Compound 3 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of HDAC8 in Complex with Compound 3 (pdb code 6odb). 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 3, PDB code: 6odb:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6odb

Go back to Potassium Binding Sites List in 6odb
Potassium binding site 1 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:38.5
occ:1.00
 O A:PHE189 2.6 30.5 1.0
O A:VAL195 2.6 38.9 1.0
O A:HOH517 2.6 34.5 1.0
O A:TYR225 2.6 39.9 1.0
O A:HOH538 2.6 40.1 1.0
O A:THR192 2.6 40.2 1.0
C A:TYR225 3.5 38.1 1.0
C A:PHE189 3.6 35.4 1.0
CB A:TYR225 3.6 40.0 1.0
C A:VAL195 3.8 37.9 1.0
C A:THR192 3.9 37.5 1.0
CB A:PHE189 4.1 34.8 1.0
CA A:TYR225 4.1 40.6 1.0
OG A:SER226 4.3 42.5 1.0
CA A:SER190 4.3 41.4 1.0
N A:SER190 4.4 38.1 1.0
CA A:MET196 4.4 42.5 1.0
N A:SER226 4.4 35.2 1.0
O A:GLY222 4.4 50.4 1.0
O A:SER190 4.5 50.8 1.0
C A:SER190 4.5 43.8 1.0
CA A:PHE189 4.5 34.4 1.0
N A:THR192 4.5 40.5 1.0
CG2 A:THR192 4.5 38.0 1.0
N A:MET196 4.5 40.8 1.0
N A:THR197 4.6 37.3 1.0
CA A:THR192 4.7 37.5 1.0
CA A:GLY222 4.8 52.1 1.0
CA A:VAL195 4.8 38.2 1.0
N A:SER193 4.9 37.6 1.0
CG A:TYR225 4.9 41.1 1.0
CA A:SER226 4.9 35.9 1.0
C A:MET196 5.0 41.4 1.0
N A:VAL195 5.0 39.0 1.0
CB A:VAL195 5.0 38.6 1.0

Potassium binding site 2 out of 6 in 6odb

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


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:29.5
occ:1.00
 O A:LEU200 2.6 31.1 1.0
O A:ASP178 2.6 31.8 1.0
OD1 A:ASP176 2.6 28.5 1.0
O A:ASP176 2.6 28.6 1.0
O A:HIS180 2.6 32.2 1.0
OG A:SER199 2.6 36.4 1.0
C A:ASP176 3.4 28.4 1.0
CG A:ASP176 3.4 29.6 1.0
C A:ASP178 3.5 30.2 1.0
N A:ASP178 3.5 25.2 1.0
C A:LEU200 3.6 32.7 1.0
C A:HIS180 3.7 34.9 1.0
CB A:ASP176 3.9 28.2 1.0
CA A:ASP178 3.9 28.0 1.0
CB A:HIS201 3.9 34.8 1.0
N A:LEU200 3.9 34.4 1.0
CB A:SER199 4.0 36.7 1.0
C A:LEU177 4.0 24.6 1.0
CB A:ASP178 4.0 31.1 1.0
N A:LEU177 4.0 26.8 1.0
CA A:LEU177 4.2 25.7 1.0
CA A:ASP176 4.3 28.6 1.0
CA A:SER199 4.3 35.3 1.0
ND1 A:HIS201 4.3 41.5 1.0
CA A:HIS201 4.4 33.0 1.0
OD2 A:ASP176 4.4 31.2 1.0
N A:HIS201 4.4 31.2 1.0
CA A:LEU200 4.4 33.3 1.0
N A:HIS181 4.4 33.8 1.0
N A:HIS180 4.4 32.9 1.0
C A:SER199 4.4 34.5 1.0
O A:HOH510 4.4 25.2 1.0
N A:GLY182 4.5 36.2 1.0
CA A:HIS181 4.5 35.3 1.0
CG A:HIS201 4.6 37.9 1.0
N A:LEU179 4.6 33.9 1.0
C A:LEU179 4.6 33.0 1.0
O A:LEU177 4.7 24.9 1.0
CA A:HIS180 4.7 33.5 1.0
C A:HIS181 4.8 35.9 1.0
O A:LEU179 4.9 34.9 1.0
CE1 A:HIS142 5.0 32.2 1.0

Potassium binding site 3 out of 6 in 6odb

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


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:47.2
occ:1.00
 O B:PHE189 2.6 48.0 1.0
O B:VAL195 2.6 43.9 1.0
O B:HOH518 2.6 40.0 1.0
O B:TYR225 2.7 45.2 1.0
O B:THR192 2.7 52.5 1.0
C B:PHE189 3.5 44.9 1.0
C B:TYR225 3.5 42.9 1.0
CB B:TYR225 3.7 44.6 1.0
C B:VAL195 3.8 44.9 1.0
C B:THR192 3.9 47.8 1.0
CB B:PHE189 4.0 49.6 1.0
CA B:TYR225 4.2 44.0 1.0
OG B:SER226 4.2 41.2 1.0
CA B:SER190 4.2 45.4 1.0
N B:SER190 4.3 45.8 1.0
CA B:PHE189 4.4 45.9 1.0
C B:SER190 4.4 46.1 1.0
CA B:MET196 4.4 43.2 1.0
O B:SER190 4.4 47.5 1.0
O B:GLY222 4.4 49.3 1.0
N B:SER226 4.4 39.5 1.0
N B:THR192 4.5 51.8 1.0
CG2 B:THR192 4.6 51.0 1.0
N B:MET196 4.6 41.8 1.0
N B:THR197 4.7 38.3 1.0
CA B:THR192 4.8 48.5 1.0
CA B:GLY222 4.8 48.4 1.0
CA B:VAL195 4.8 45.1 1.0
N B:SER193 4.9 49.2 1.0
CA B:SER226 4.9 38.4 1.0
CB B:VAL195 5.0 45.6 1.0
CG B:TYR225 5.0 50.0 1.0

Potassium binding site 4 out of 6 in 6odb

Go back to Potassium Binding Sites List in 6odb
Potassium binding site 4 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:33.5
occ:1.00
 OD1 B:ASP176 2.6 36.2 1.0
O B:ASP178 2.6 36.5 1.0
O B:LEU200 2.6 31.1 1.0
O B:ASP176 2.6 36.8 1.0
O B:HIS180 2.6 33.6 1.0
OG B:SER199 2.6 41.4 1.0
C B:ASP176 3.4 36.1 1.0
CG B:ASP176 3.4 37.3 1.0
C B:ASP178 3.4 37.2 1.0
N B:ASP178 3.5 34.7 1.0
C B:LEU200 3.6 31.8 1.0
C B:HIS180 3.7 36.7 1.0
CA B:ASP178 3.8 36.1 1.0
CB B:ASP176 3.9 35.2 1.0
N B:LEU200 3.9 36.1 1.0
C B:LEU177 3.9 34.9 1.0
CB B:HIS201 3.9 31.4 1.0
CB B:SER199 4.0 39.9 1.0
CB B:ASP178 4.0 40.2 1.0
N B:LEU177 4.0 35.7 1.0
CA B:LEU177 4.2 35.1 1.0
CA B:ASP176 4.2 34.5 1.0
CA B:SER199 4.3 37.9 1.0
O B:HOH503 4.3 33.5 1.0
OD2 B:ASP176 4.4 36.7 1.0
ND1 B:HIS201 4.4 34.2 1.0
N B:HIS180 4.4 36.0 1.0
CA B:LEU200 4.4 34.4 1.0
N B:HIS201 4.4 30.5 1.0
CA B:HIS201 4.4 30.9 1.0
N B:HIS181 4.4 35.3 1.0
C B:SER199 4.5 37.5 1.0
N B:GLY182 4.5 36.3 1.0
CA B:HIS181 4.5 35.5 1.0
N B:LEU179 4.6 38.7 1.0
C B:LEU179 4.6 36.5 1.0
CG B:HIS201 4.6 32.7 1.0
O B:LEU177 4.7 33.0 1.0
CA B:HIS180 4.7 37.0 1.0
C B:HIS181 4.8 35.8 1.0
CE1 B:HIS142 4.9 37.4 1.0
O B:LEU179 4.9 36.9 1.0

Potassium binding site 5 out of 6 in 6odb

Go back to Potassium Binding Sites List in 6odb
Potassium binding site 5 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:59.3
occ:1.00
 O C:PHE189 2.6 46.7 1.0
O C:HOH506 2.6 54.6 1.0
O C:VAL195 2.6 51.9 1.0
O C:TYR225 2.6 60.4 1.0
O C:THR192 2.6 63.0 1.0
C C:TYR225 3.5 63.6 1.0
C C:PHE189 3.6 50.2 1.0
CB C:TYR225 3.6 61.1 1.0
C C:VAL195 3.8 51.6 1.0
C C:THR192 3.9 60.9 1.0
CB C:PHE189 4.1 51.8 1.0
CA C:TYR225 4.1 64.5 1.0
OG C:SER226 4.2 50.9 1.0
CA C:SER190 4.2 58.6 1.0
N C:SER190 4.3 53.0 1.0
N C:SER226 4.4 60.5 1.0
O C:GLY222 4.4 70.6 1.0
O C:SER190 4.4 66.5 1.0
C C:SER190 4.4 62.8 1.0
CA C:MET196 4.4 53.0 1.0
CA C:PHE189 4.5 49.8 1.0
N C:THR192 4.5 60.0 1.0
CG2 C:THR192 4.6 54.9 1.0
N C:MET196 4.6 50.5 1.0
N C:THR197 4.7 52.5 1.0
CA C:GLY222 4.7 72.8 1.0
CA C:THR192 4.7 57.5 1.0
N C:SER193 4.9 60.9 1.0
CA C:VAL195 4.9 56.6 1.0
CG C:TYR225 4.9 60.4 1.0
CA C:SER226 4.9 55.4 1.0

Potassium binding site 6 out of 6 in 6odb

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


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K404

b:49.9
occ:1.00
 O C:HIS180 2.6 45.2 1.0
O C:LEU200 2.6 47.5 1.0
OD1 C:ASP176 2.6 50.4 1.0
O C:ASP176 2.6 45.3 1.0
O C:ASP178 2.6 51.2 1.0
OG C:SER199 2.6 64.0 1.0
C C:ASP176 3.4 47.7 1.0
CG C:ASP176 3.4 53.1 1.0
C C:ASP178 3.5 47.0 1.0
N C:ASP178 3.6 45.4 1.0
C C:LEU200 3.6 51.5 1.0
C C:HIS180 3.7 50.4 1.0
CB C:ASP176 3.9 48.3 1.0
CB C:HIS201 3.9 56.5 1.0
CA C:ASP178 3.9 44.1 1.0
N C:LEU200 3.9 56.3 1.0
CB C:SER199 4.0 57.4 1.0
C C:LEU177 4.0 44.8 1.0
CB C:ASP178 4.0 42.3 1.0
N C:LEU177 4.1 44.5 1.0
CA C:LEU177 4.2 45.4 1.0
CA C:ASP176 4.2 50.4 1.0
CA C:SER199 4.3 58.8 1.0
OD2 C:ASP176 4.3 52.7 1.0
ND1 C:HIS201 4.4 61.0 1.0
N C:HIS181 4.4 56.0 1.0
CA C:HIS201 4.4 52.5 1.0
N C:GLY182 4.4 59.2 1.0
N C:HIS180 4.4 52.0 1.0
N C:HIS201 4.4 49.6 1.0
CA C:LEU200 4.4 55.2 1.0
CA C:HIS181 4.4 58.6 1.0
C C:SER199 4.5 54.5 1.0
CG C:HIS201 4.6 60.0 1.0
C C:LEU179 4.6 50.4 1.0
N C:LEU179 4.6 48.3 1.0
CA C:HIS180 4.7 51.5 1.0
C C:HIS181 4.7 58.2 1.0
O C:LEU177 4.7 47.8 1.0
O C:HOH501 4.8 39.4 1.0
CE1 C:HIS142 4.9 61.4 1.0
O C:LEU179 4.9 46.5 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.
Page generated: Sat Aug 9 11:42:32 2025

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