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Potassium in PDB 6odc: Crystal Structure of HDAC8 in Complex with Compound 30

Enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 30

All present enzymatic activity of Crystal Structure of HDAC8 in Complex with Compound 30:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of HDAC8 in Complex with Compound 30, PDB code: 6odc 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.540, 91.161, 92.574, 90.00, 94.07, 90.00
R / Rfree (%) 19.4 / 23.6

Other elements in 6odc:

The structure of Crystal Structure of HDAC8 in Complex with Compound 30 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 30 (pdb code 6odc). 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 30, PDB code: 6odc:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6odc

Go back to Potassium Binding Sites List in 6odc
Potassium binding site 1 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 30


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 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:57.7
occ:1.00
 O A:PHE189 2.6 62.8 1.0
O A:VAL195 2.6 58.9 1.0
O A:HOH503 2.6 60.1 1.0
O A:HOH506 2.6 57.1 1.0
O A:TYR225 2.6 58.4 1.0
O A:THR192 2.7 60.5 1.0
C A:TYR225 3.6 63.5 1.0
C A:PHE189 3.6 60.5 1.0
CB A:TYR225 3.7 67.5 1.0
C A:VAL195 3.8 60.0 1.0
C A:THR192 3.9 64.1 1.0
CB A:PHE189 4.0 62.4 1.0
CA A:TYR225 4.3 61.3 1.0
OG A:SER226 4.4 60.7 1.0
N A:SER190 4.4 62.6 1.0
CA A:SER190 4.4 63.4 1.0
CA A:MET196 4.4 58.3 1.0
CA A:PHE189 4.4 61.2 1.0
N A:SER226 4.5 60.0 1.0
CG2 A:THR192 4.5 61.4 1.0
N A:THR192 4.5 71.1 1.0
N A:MET196 4.6 58.8 1.0
C A:SER190 4.6 67.4 1.0
O A:SER190 4.6 73.5 1.0
O A:GLY222 4.6 53.9 1.0
N A:THR197 4.6 54.3 1.0
CA A:THR192 4.7 62.9 1.0
CA A:VAL195 4.8 62.5 1.0
CA A:GLY222 4.8 64.7 1.0
N A:SER193 4.8 67.6 1.0
CG2 A:THR197 4.9 48.3 1.0
CB A:VAL195 4.9 63.4 1.0
N A:VAL195 5.0 70.9 1.0
C A:MET196 5.0 57.5 1.0

Potassium binding site 2 out of 6 in 6odc

Go back to Potassium Binding Sites List in 6odc
Potassium binding site 2 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 30


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

b:57.7
occ:1.00
 OD1 A:ASP176 2.6 52.7 1.0
O A:ASP176 2.6 55.8 1.0
O A:LEU200 2.6 60.6 1.0
O A:ASP178 2.6 65.0 1.0
OG A:SER199 2.6 64.8 1.0
O A:HIS180 2.6 52.3 1.0
C A:ASP176 3.4 53.5 1.0
CG A:ASP176 3.4 51.4 1.0
C A:LEU200 3.5 54.6 1.0
C A:ASP178 3.6 55.9 1.0
N A:ASP178 3.7 50.3 1.0
C A:HIS180 3.7 54.7 1.0
CB A:ASP176 3.8 49.5 1.0
N A:LEU200 3.8 51.4 1.0
CB A:SER199 3.9 58.8 1.0
CB A:HIS201 4.0 54.5 1.0
CA A:ASP178 4.0 54.2 1.0
N A:LEU177 4.0 52.8 1.0
C A:LEU177 4.1 52.6 1.0
CB A:ASP178 4.2 60.4 1.0
ND1 A:HIS201 4.2 54.0 1.0
CA A:ASP176 4.2 53.7 1.0
CA A:SER199 4.2 54.2 1.0
CA A:LEU177 4.2 52.4 1.0
N A:GLY182 4.3 51.4 1.0
OD2 A:ASP176 4.3 48.2 1.0
C A:SER199 4.3 51.9 1.0
N A:HIS201 4.3 53.6 1.0
CA A:LEU200 4.3 55.4 1.0
CA A:HIS181 4.4 49.7 1.0
N A:HIS181 4.4 52.5 1.0
CA A:HIS201 4.4 53.8 1.0
CG A:HIS201 4.5 57.5 1.0
N A:HIS180 4.5 51.9 1.0
C A:LEU179 4.6 51.4 1.0
C A:HIS181 4.7 51.3 1.0
N A:LEU179 4.7 57.4 1.0
CA A:HIS180 4.7 52.7 1.0
O A:LEU179 4.8 52.8 1.0
O A:LEU177 4.9 53.2 1.0
CE1 A:HIS142 5.0 53.3 1.0

Potassium binding site 3 out of 6 in 6odc

Go back to Potassium Binding Sites List in 6odc
Potassium binding site 3 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 30


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 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:51.7
occ:1.00
 O B:PHE189 2.6 47.2 1.0
O B:VAL195 2.6 53.6 1.0
O B:HOH506 2.6 49.2 1.0
O B:TYR225 2.6 54.9 1.0
O B:HOH520 2.6 54.7 1.0
O B:THR192 2.6 51.3 1.0
C B:TYR225 3.5 60.9 1.0
C B:PHE189 3.6 58.6 1.0
CB B:TYR225 3.6 57.0 1.0
C B:VAL195 3.8 57.1 1.0
C B:THR192 3.8 54.5 1.0
CB B:PHE189 4.1 48.6 1.0
CA B:TYR225 4.2 61.2 1.0
CA B:SER190 4.3 62.6 1.0
OG B:SER226 4.4 54.6 1.0
N B:SER190 4.4 63.0 1.0
N B:SER226 4.4 57.3 1.0
CA B:MET196 4.4 54.5 1.0
N B:THR192 4.5 51.0 1.0
CA B:PHE189 4.5 51.4 1.0
O B:GLY222 4.5 64.2 1.0
CG2 B:THR192 4.5 60.5 1.0
C B:SER190 4.5 64.8 1.0
O B:SER190 4.5 68.8 1.0
N B:MET196 4.6 54.2 1.0
CA B:THR192 4.7 56.9 1.0
N B:THR197 4.7 59.3 1.0
CA B:GLY222 4.8 70.5 1.0
N B:SER193 4.8 55.7 1.0
CA B:VAL195 4.8 64.0 1.0
CG B:TYR225 4.9 57.0 1.0
CG2 B:THR197 5.0 61.0 1.0
N B:VAL195 5.0 70.3 1.0
CB B:VAL195 5.0 68.1 1.0
CA B:SER193 5.0 57.1 1.0
CA B:SER226 5.0 53.8 1.0

Potassium binding site 4 out of 6 in 6odc

Go back to Potassium Binding Sites List in 6odc
Potassium binding site 4 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 30


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

b:50.4
occ:1.00
 O B:LEU200 2.6 48.5 1.0
O B:ASP176 2.6 52.1 1.0
O B:ASP178 2.6 52.5 1.0
O B:HIS180 2.6 41.5 1.0
OD1 B:ASP176 2.6 50.0 1.0
OG B:SER199 2.6 51.2 1.0
C B:ASP176 3.4 47.3 1.0
CG B:ASP176 3.4 50.6 1.0
C B:LEU200 3.5 48.0 1.0
C B:ASP178 3.6 51.4 1.0
N B:ASP178 3.7 42.9 1.0
C B:HIS180 3.7 48.7 1.0
CB B:ASP176 3.8 47.0 1.0
N B:LEU200 3.8 47.6 1.0
CB B:SER199 3.9 50.0 1.0
CB B:HIS201 3.9 51.0 1.0
CA B:ASP178 4.0 48.2 1.0
N B:LEU177 4.1 44.6 1.0
C B:LEU177 4.1 43.2 1.0
CB B:ASP178 4.2 49.5 1.0
ND1 B:HIS201 4.2 60.1 1.0
CA B:ASP176 4.2 49.4 1.0
CA B:SER199 4.2 51.0 1.0
N B:GLY182 4.2 48.3 1.0
CA B:LEU177 4.3 44.2 1.0
OD2 B:ASP176 4.3 49.6 1.0
N B:HIS201 4.3 46.8 1.0
C B:SER199 4.3 50.5 1.0
CA B:LEU200 4.3 46.5 1.0
CA B:HIS181 4.4 48.7 1.0
CA B:HIS201 4.4 50.9 1.0
N B:HIS181 4.4 50.1 1.0
CG B:HIS201 4.5 55.3 1.0
N B:HIS180 4.5 46.9 1.0
O B:HOH504 4.6 44.1 1.0
C B:LEU179 4.6 50.0 1.0
C B:HIS181 4.6 50.5 1.0
N B:LEU179 4.7 55.6 1.0
CA B:HIS180 4.7 49.4 1.0
O B:LEU179 4.8 45.2 1.0
O B:LEU177 4.9 47.2 1.0
CE1 B:HIS142 5.0 57.6 1.0

Potassium binding site 5 out of 6 in 6odc

Go back to Potassium Binding Sites List in 6odc
Potassium binding site 5 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 30


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 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:77.0
occ:1.00
 O C:PHE189 2.6 66.8 1.0
O C:HOH501 2.6 60.4 1.0
O C:VAL195 2.6 65.0 1.0
O C:TYR225 2.6 83.2 1.0
O C:HOH507 2.6 77.3 1.0
O C:THR192 2.6 89.2 1.0
C C:TYR225 3.5 94.2 1.0
C C:PHE189 3.6 72.8 1.0
CB C:TYR225 3.7 96.7 1.0
C C:VAL195 3.8 76.3 1.0
C C:THR192 3.8 79.2 1.0
CB C:PHE189 4.1 72.2 1.0
CA C:TYR225 4.2 93.9 1.0
CA C:SER190 4.4 75.8 1.0
OG C:SER226 4.4 74.2 1.0
N C:SER190 4.4 69.6 1.0
CA C:MET196 4.4 79.4 1.0
N C:SER226 4.4 92.9 1.0
CA C:PHE189 4.5 73.0 1.0
CG2 C:THR192 4.5 81.0 1.0
N C:THR192 4.5 83.4 1.0
O C:GLY222 4.5 92.7 1.0
C C:SER190 4.5 85.8 1.0
O C:SER190 4.6 93.2 1.0
N C:MET196 4.6 79.3 1.0
N C:THR197 4.7 75.5 1.0
CA C:THR192 4.7 81.6 1.0
CA C:GLY222 4.8 91.7 1.0
N C:SER193 4.8 79.0 1.0
CA C:VAL195 4.8 82.8 1.0
CG2 C:THR197 4.9 82.0 1.0
N C:VAL195 5.0 89.9 1.0
CG C:TYR225 5.0 99.6 1.0
CB C:VAL195 5.0 84.5 1.0

Potassium binding site 6 out of 6 in 6odc

Go back to Potassium Binding Sites List in 6odc
Potassium binding site 6 out of 6 in the Crystal Structure of HDAC8 in Complex with Compound 30


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

b:67.0
occ:1.00
 O C:ASP176 2.6 58.9 1.0
O C:ASP178 2.6 63.8 1.0
O C:LEU200 2.6 65.1 1.0
OD1 C:ASP176 2.6 72.5 1.0
O C:HIS180 2.6 58.1 1.0
OG C:SER199 2.6 84.6 1.0
C C:ASP176 3.3 68.4 1.0
CG C:ASP176 3.3 72.7 1.0
C C:LEU200 3.6 66.5 1.0
C C:ASP178 3.6 60.5 1.0
N C:ASP178 3.7 59.6 1.0
C C:HIS180 3.7 59.7 1.0
CB C:ASP176 3.8 68.4 1.0
N C:LEU200 3.9 78.8 1.0
CB C:SER199 3.9 80.6 1.0
CB C:HIS201 4.0 80.8 1.0
CA C:ASP178 4.0 55.8 1.0
N C:LEU177 4.0 67.3 1.0
C C:LEU177 4.1 62.9 1.0
CB C:ASP178 4.2 57.0 1.0
CA C:ASP176 4.2 73.6 1.0
ND1 C:HIS201 4.2 86.0 1.0
CA C:SER199 4.2 84.2 1.0
CA C:LEU177 4.2 65.3 1.0
N C:GLY182 4.3 63.7 1.0
OD2 C:ASP176 4.3 75.0 1.0
C C:SER199 4.4 78.4 1.0
N C:HIS201 4.4 71.2 1.0
CA C:LEU200 4.4 72.5 1.0
CA C:HIS181 4.4 71.5 1.0
CA C:HIS201 4.4 76.0 1.0
N C:HIS181 4.4 67.9 1.0
O C:HOH502 4.5 51.2 1.0
N C:HIS180 4.5 63.4 1.0
CG C:HIS201 4.5 84.7 1.0
C C:LEU179 4.6 68.0 1.0
C C:HIS181 4.7 71.4 1.0
N C:LEU179 4.7 64.7 1.0
CA C:HIS180 4.7 61.9 1.0
O C:LEU179 4.8 66.0 1.0
O C:LEU177 4.9 73.3 1.0
CE1 C:HIS142 5.0 72.9 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: Mon Dec 14 01:01:57 2020

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