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Chlorine in PDB 5oul: The Crystal Structure of CK2ALPHA in Complex with Compound 9

Enzymatic activity of The Crystal Structure of CK2ALPHA in Complex with Compound 9

All present enzymatic activity of The Crystal Structure of CK2ALPHA in Complex with Compound 9:
2.7.11.1;

Protein crystallography data

The structure of The Crystal Structure of CK2ALPHA in Complex with Compound 9, PDB code: 5oul was solved by P.Brear, C.De Fusco, J.Iegre, M.Yoshida, S.Mitchell, M.Rossmann, L.Carro, H.Sore, M.Hyvonen, D.Spring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.59 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.703, 46.080, 63.369, 90.00, 112.39, 90.00
R / Rfree (%) 19.8 / 22.2

Other elements in 5oul:

The structure of The Crystal Structure of CK2ALPHA in Complex with Compound 9 also contains other interesting chemical elements:

Fluorine (F) 11 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of CK2ALPHA in Complex with Compound 9 (pdb code 5oul). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the The Crystal Structure of CK2ALPHA in Complex with Compound 9, PDB code: 5oul:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5oul

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Chlorine binding site 1 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:35.9
occ:0.50
 CL A:AWE403 0.0 35.9 0.5
C5 A:AWE403 1.7 32.1 0.5
C3 A:AWE403 1.7 32.9 0.5
C2 A:AWE403 2.5 34.3 0.5
C6 A:AWE403 2.7 31.5 0.5
C4 A:AWE403 2.7 28.4 0.5
C4 A:AWE403 2.7 31.5 0.5
C7 A:AWE403 3.1 30.2 0.5
SD A:MET225 3.2 27.0 0.5
C7 A:AWE403 3.2 29.2 0.5
C12 A:AWE403 3.5 33.0 0.5
CE A:MET225 3.7 22.1 0.5
C8 A:AWE403 3.7 26.8 0.5
C1 A:AWE403 3.8 34.9 0.5
C12 A:AWE403 3.9 30.0 0.5
CD1 A:LEU128 3.9 33.9 1.0
C5 A:AWE403 3.9 34.2 0.5
C8 A:AWE403 3.9 33.0 0.5
CA A:TYR125 3.9 27.9 1.0
C1 A:AWE403 4.0 29.9 0.5
N A:TYR125 4.0 29.0 1.0
C3 A:AWE403 4.0 25.2 0.5
O A:HOH703 4.2 55.4 1.0
SD A:MET225 4.2 31.7 0.5
C A:LEU124 4.3 35.0 1.0
C6 A:AWE403 4.3 33.1 0.5
CE1 A:PHE121 4.4 55.9 1.0
CB A:TYR125 4.4 30.9 1.0
CB A:LEU124 4.5 39.3 1.0
CD1 A:PHE121 4.5 55.1 1.0
CG A:MET225 4.5 25.7 0.5
C2 A:AWE403 4.5 24.1 0.5
CG A:MET225 4.5 22.1 0.5
C11 A:AWE403 4.5 36.8 0.5
CD2 A:LEU124 4.6 47.2 1.0
O A:LEU124 4.6 33.2 1.0
CG A:LEU124 4.7 45.3 1.0
CG A:LEU128 4.7 33.5 1.0
C9 A:AWE403 4.7 25.1 0.5
C11 A:AWE403 4.8 31.1 0.5
C9 A:AWE403 4.9 35.9 0.5
CD1 A:TYR125 4.9 37.2 1.0
O A:PHE121 4.9 48.4 1.0
C A:AWE403 5.0 35.5 0.5

Chlorine binding site 2 out of 8 in 5oul

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Chlorine binding site 2 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.7
occ:0.50
 CL A:AWE403 0.0 39.7 0.5
C5 A:AWE403 1.7 34.2 0.5
C3 A:AWE403 1.8 25.2 0.5
C6 A:AWE403 2.7 33.1 0.5
C4 A:AWE403 2.7 31.5 0.5
C4 A:AWE403 2.7 28.4 0.5
CE A:MET221 2.7 20.6 1.0
C2 A:AWE403 2.8 24.1 0.5
C7 A:AWE403 2.9 30.2 0.5
C8 A:AWE403 3.0 33.0 0.5
C7 A:AWE403 3.1 29.2 0.5
CB A:VAL162 3.1 17.9 1.0
CG1 A:VAL162 3.2 18.6 1.0
C12 A:AWE403 3.3 30.0 0.5
CG2 A:VAL162 3.4 17.6 1.0
CD1 A:ILE140 3.7 16.1 1.0
C12 A:AWE403 3.9 33.0 0.5
C5 A:AWE403 4.0 32.1 0.5
C3 A:AWE403 4.0 32.9 0.5
C1 A:AWE403 4.0 34.9 0.5
C9 A:AWE403 4.0 35.9 0.5
C8 A:AWE403 4.0 26.8 0.5
C1 A:AWE403 4.1 29.9 0.5
CA A:PRO159 4.1 15.6 1.0
SD A:MET221 4.2 23.3 1.0
C11 A:AWE403 4.3 31.1 0.5
O A:PRO159 4.5 16.5 1.0
C2 A:AWE403 4.5 34.3 0.5
C6 A:AWE403 4.5 31.5 0.5
CA A:VAL162 4.5 14.6 1.0
CD1 A:ILE164 4.6 27.8 1.0
C11 A:AWE403 4.7 36.8 0.5
O A:VAL162 4.7 18.9 1.0
CB A:PRO159 4.7 18.5 1.0
C10 A:AWE403 4.8 37.2 0.5
CG1 A:ILE140 4.8 14.0 1.0
C A:PRO159 4.8 17.2 1.0
C9 A:AWE403 4.9 25.1 0.5
O A:LYS158 4.9 12.4 1.0
N A:PRO159 5.0 14.7 1.0

Chlorine binding site 3 out of 8 in 5oul

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Chlorine binding site 3 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:32.0
occ:0.50
 CL A:AWE404 0.0 32.0 0.5
C3 A:AWE404 1.7 75.8 0.5
C5 A:AWE404 1.7 25.3 0.5
C4 A:AWE404 2.5 75.9 0.5
C6 A:AWE404 2.7 22.9 0.5
C2 A:AWE404 2.7 75.6 0.5
C4 A:AWE404 2.7 24.4 0.5
C7 A:AWE404 2.8 76.7 0.5
C12 A:AWE404 3.1 77.5 0.5
C7 A:AWE404 3.1 29.4 0.5
C8 A:AWE404 3.5 32.7 0.5
C8 A:AWE404 3.7 77.0 0.5
C5 A:AWE404 3.7 75.5 0.5
F A:AWE405 3.8 43.2 1.0
CD A:PRO295 3.9 18.6 1.0
C1 A:AWE404 3.9 75.5 0.5
CG A:PRO295 3.9 23.6 1.0
C12 A:AWE404 4.0 31.0 0.5
C1 A:AWE404 4.0 20.2 0.5
C3 A:AWE404 4.0 22.8 0.5
C11 A:AWE404 4.2 77.9 0.5
C6 A:AWE404 4.3 75.2 0.5
C2 A:AWE404 4.5 18.8 0.5
C9 A:AWE404 4.5 34.2 0.5
C11 A:AWE405 4.6 43.4 1.0
C9 A:AWE404 4.6 77.3 0.5
C11 A:AWE404 4.8 32.8 0.5
C10 A:AWE404 4.9 77.7 0.5
C10 A:AWE405 4.9 43.0 1.0
N A:PRO295 5.0 15.6 1.0
F A:AWE404 5.0 77.9 0.5

Chlorine binding site 4 out of 8 in 5oul

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Chlorine binding site 4 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:75.3
occ:0.50
 CL A:AWE404 0.0 75.3 0.5
C3 A:AWE404 1.3 22.8 0.5
C5 A:AWE404 1.7 75.5 0.5
C2 A:AWE404 2.1 18.8 0.5
C4 A:AWE404 2.4 24.4 0.5
C6 A:AWE404 2.7 75.2 0.5
C4 A:AWE404 2.7 75.9 0.5
C7 A:AWE404 3.0 29.4 0.5
C7 A:AWE404 3.1 76.7 0.5
C1 A:AWE404 3.4 20.2 0.5
CG1 A:VAL285 3.5 16.1 1.0
C8 A:AWE405 3.5 43.1 1.0
C5 A:AWE404 3.6 25.3 0.5
CG1 A:VAL293 3.6 21.1 1.0
C12 A:AWE404 3.6 77.5 0.5
C8 A:AWE404 3.6 77.0 0.5
C7 A:AWE405 3.7 41.9 1.0
C12 A:AWE404 3.7 31.0 0.5
C9 A:AWE405 3.7 43.5 1.0
C8 A:AWE404 3.7 32.7 0.5
CL A:AWE405 3.8 43.7 1.0
CB A:VAL293 3.9 19.9 1.0
C12 A:AWE405 3.9 43.2 1.0
C6 A:AWE404 3.9 22.9 0.5
C10 A:AWE405 4.0 43.0 1.0
C1 A:AWE404 4.0 75.5 0.5
C3 A:AWE404 4.0 75.8 0.5
C11 A:AWE405 4.0 43.4 1.0
CG2 A:VAL285 4.1 16.5 1.0
CB A:VAL285 4.4 16.2 1.0
C4 A:AWE405 4.4 40.0 1.0
C2 A:AWE404 4.5 75.6 0.5
O A:GLN290 4.5 18.9 1.0
C11 A:AWE404 4.5 77.9 0.5
C5 A:AWE405 4.5 38.6 1.0
C9 A:AWE404 4.5 77.3 0.5
C A:VAL293 4.6 18.7 1.0
O A:VAL293 4.6 20.0 1.0
C A:AWE404 4.6 19.0 0.5
CB A:GLN290 4.6 19.4 1.0
C11 A:AWE404 4.7 32.8 0.5
C9 A:AWE404 4.8 34.2 0.5
CA A:GLN290 4.8 17.4 1.0
F A:AWE405 4.8 43.2 1.0
CA A:VAL293 4.8 15.8 1.0
CG2 A:VAL293 4.9 18.6 1.0
N A:SER294 4.9 15.1 1.0
C10 A:AWE404 4.9 77.7 0.5

Chlorine binding site 5 out of 8 in 5oul

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Chlorine binding site 5 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:43.7
occ:1.00
 CL A:AWE405 0.0 43.7 1.0
C5 A:AWE405 1.7 38.6 1.0
C6 A:AWE405 2.7 32.9 1.0
C4 A:AWE405 2.7 40.0 1.0
C7 A:AWE405 3.2 41.9 1.0
C12 A:AWE405 3.2 43.2 1.0
F A:AWE404 3.4 77.9 0.5
C11 A:AWE404 3.4 77.9 0.5
C8 A:AWE404 3.4 32.7 0.5
C9 A:AWE404 3.5 34.2 0.5
C12 A:AWE404 3.7 77.5 0.5
CL A:AWE404 3.8 75.3 0.5
CB A:GLU282 3.9 20.2 1.0
C10 A:AWE404 3.9 77.7 0.5
C1 A:AWE405 4.0 33.0 1.0
C3 A:AWE405 4.0 39.7 1.0
C7 A:AWE404 4.1 29.4 0.5
CB A:VAL285 4.1 16.2 1.0
CG2 A:VAL285 4.1 16.5 1.0
CG1 A:VAL285 4.1 16.1 1.0
C10 A:AWE404 4.2 33.9 0.5
C8 A:AWE405 4.3 43.1 1.0
C7 A:AWE404 4.3 76.7 0.5
C11 A:AWE405 4.4 43.4 1.0
C2 A:AWE405 4.5 35.7 1.0
C9 A:AWE404 4.5 77.3 0.5
O A:GLU282 4.6 19.8 1.0
C3 A:AWE404 4.6 22.8 0.5
CA A:GLU282 4.6 17.2 1.0
C12 A:AWE404 4.7 31.0 0.5
C11 A:AWE404 4.7 32.8 0.5
C4 A:AWE404 4.7 24.4 0.5
C8 A:AWE404 4.7 77.0 0.5
F A:AWE405 4.9 43.2 1.0
C5 A:AWE404 5.0 75.5 0.5

Chlorine binding site 6 out of 8 in 5oul

Go back to Chlorine Binding Sites List in 5oul
Chlorine binding site 6 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:40.3
occ:1.00
 CL A:AWE406 0.0 40.3 1.0
C5 A:AWE406 1.7 42.9 1.0
C6 A:AWE406 2.7 44.8 1.0
C4 A:AWE406 2.8 42.9 1.0
C7 A:AWE406 3.2 40.8 1.0
C12 A:AWE406 3.4 39.5 1.0
O A:ILE69 3.5 16.5 1.0
CG A:LYS71 3.6 26.5 1.0
CG2 A:ILE69 3.8 16.2 1.0
C1 A:AWE406 4.0 45.6 1.0
O A:LEU70 4.0 23.0 1.0
C3 A:AWE406 4.0 44.9 1.0
CB A:GLU52 4.1 21.5 1.0
C A:LEU70 4.2 21.6 1.0
C A:ILE69 4.2 17.3 1.0
CB A:ILE69 4.2 14.9 1.0
CA A:LYS71 4.2 20.8 1.0
C8 A:AWE406 4.3 38.7 1.0
N A:LYS71 4.3 19.6 1.0
N A:GLU52 4.4 18.8 1.0
OE1 A:GLU52 4.5 48.0 1.0
C2 A:AWE406 4.5 43.9 1.0
CB A:LYS71 4.5 21.5 1.0
CB A:SER106 4.6 17.9 1.0
C11 A:AWE406 4.6 41.7 1.0
CE A:LYS71 4.6 47.6 1.0
CD A:LYS71 4.7 34.5 1.0
CA A:ILE69 4.9 12.5 1.0
N A:LEU70 4.9 16.7 1.0
C A:SER51 4.9 22.2 1.0
CA A:GLU52 4.9 19.4 1.0

Chlorine binding site 7 out of 8 in 5oul

Go back to Chlorine Binding Sites List in 5oul
Chlorine binding site 7 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:58.7
occ:1.00
 CL A:AWE407 0.0 58.7 1.0
C5 A:AWE407 1.7 50.3 1.0
C6 A:AWE407 2.7 50.8 1.0
C4 A:AWE407 2.7 45.1 1.0
C7 A:AWE407 3.1 39.0 1.0
C8 A:AWE407 3.2 36.5 1.0
SD A:MET163 3.6 27.5 1.0
OD1 A:ASN118 4.0 42.2 1.0
C1 A:AWE407 4.0 51.3 1.0
C3 A:AWE407 4.0 46.9 1.0
CL A:AWE408 4.2 98.2 1.0
C9 A:AWE407 4.2 33.3 1.0
C12 A:AWE407 4.3 37.0 1.0
CB A:ASN118 4.3 29.9 1.0
CE A:MET163 4.3 25.2 1.0
CG A:ASN118 4.4 47.6 1.0
C6 A:AWE408 4.5 98.8 1.0
C2 A:AWE407 4.5 48.8 1.0
C5 A:AWE408 4.6 98.2 1.0

Chlorine binding site 8 out of 8 in 5oul

Go back to Chlorine Binding Sites List in 5oul
Chlorine binding site 8 out of 8 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:98.2
occ:1.00
 CL A:AWE408 0.0 98.2 1.0
C5 A:AWE408 1.7 98.2 1.0
C6 A:AWE408 2.7 98.8 1.0
C4 A:AWE408 2.7 97.9 1.0
O A:HOH509 3.0 22.3 1.0
C12 A:AWE408 3.2 97.2 1.0
C7 A:AWE408 3.2 97.3 1.0
CD2 A:HIS160 3.3 29.7 1.0
O A:HIS160 3.3 20.1 1.0
CG A:HIS160 3.6 27.1 1.0
CB A:HIS160 3.7 21.4 1.0
CE A:MET163 3.7 25.2 1.0
CA A:HIS160 3.7 19.0 1.0
C1 A:AWE408 4.0 99.8 1.0
C A:HIS160 4.0 19.1 1.0
C3 A:AWE408 4.0 98.7 1.0
NE2 A:HIS160 4.2 30.4 1.0
CL A:AWE407 4.2 58.7 1.0
C11 A:AWE408 4.3 97.0 1.0
C8 A:AWE408 4.3 97.4 1.0
C2 A:AWE408 4.5 99.4 1.0
ND1 A:HIS160 4.5 30.1 1.0
SD A:MET163 4.7 27.5 1.0
OD1 A:ASN118 4.8 42.2 1.0
CE1 A:HIS160 4.8 29.8 1.0
F A:AWE408 4.8 96.5 1.0
N A:AWE403 5.0 31.9 0.5

Reference:

J.Iegre, P.Brear, C.De Fusco, M.Yoshida, S.L.Mitchell, M.Rossmann, L.Carro, H.F.Sore, M.Hyvonen, D.R.Spring. Second-Generation CK2 Alpha Inhibitors Targeting the Alpha D Pocket. Chem Sci V. 9 3041 2018.
ISSN: ISSN 2041-6520
PubMed: 29732088
DOI: 10.1039/C7SC05122K
Page generated: Fri Jul 26 14:54:24 2024

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