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Fluorine 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:

Chlorine (Cl) 8 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 11 binding sites of Fluorine where determined in the The Crystal Structure of CK2ALPHA in Complex with Compound 9, PDB code: 5oul:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 11 in 5oul

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Fluorine binding site 1 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F403

b:40.8
occ:0.50
 F A:AWE403 0.0 40.8 0.5
C9 A:AWE403 1.0 25.1 0.5
C11 A:AWE403 1.4 36.8 0.5
C10 A:AWE403 1.9 28.6 0.5
C8 A:AWE403 2.2 26.8 0.5
C10 A:AWE403 2.3 37.2 0.5
C12 A:AWE403 2.3 33.0 0.5
C11 A:AWE403 3.2 31.1 0.5
O A:ILE133 3.2 14.3 1.0
CB A:TYR136 3.2 14.8 1.0
C7 A:AWE403 3.4 29.2 0.5
CA A:ILE133 3.4 14.7 1.0
C9 A:AWE403 3.6 35.9 0.5
SD A:MET225 3.6 31.7 0.5
C7 A:AWE403 3.6 30.2 0.5
C12 A:AWE403 3.7 30.0 0.5
C A:ILE133 3.8 16.3 1.0
N A:MET137 3.9 12.4 1.0
O A:ASP132 3.9 15.5 1.0
CD1 A:LEU128 3.9 33.9 1.0
CA A:TYR136 4.1 12.1 1.0
CE A:MET225 4.1 28.4 0.5
C8 A:AWE403 4.1 33.0 0.5
CG2 A:ILE133 4.1 15.1 1.0
C A:TYR136 4.1 14.6 1.0
CG A:MET137 4.2 15.6 1.0
CB A:ILE133 4.2 17.8 1.0
CG A:TYR136 4.2 17.1 1.0
F A:AWE403 4.3 33.8 0.5
CD2 A:TYR136 4.3 16.4 1.0
N A:ILE133 4.4 15.3 1.0
N A:TYR136 4.4 13.0 1.0
CG1 A:ILE133 4.5 18.8 1.0
C A:ASP132 4.5 16.5 1.0
C4 A:AWE403 4.7 31.5 0.5
CA A:MET137 4.7 11.6 1.0
C4 A:AWE403 4.8 28.4 0.5
CB A:MET137 4.9 13.5 1.0
O A:TYR136 4.9 14.6 1.0

Fluorine binding site 2 out of 11 in 5oul

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Fluorine binding site 2 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F403

b:33.8
occ:0.50
 F A:AWE403 0.0 33.8 0.5
C9 A:AWE403 1.2 35.9 0.5
C11 A:AWE403 1.4 31.1 0.5
CE A:MET225 1.4 28.4 0.5
C10 A:AWE403 2.0 37.2 0.5
SD A:MET225 2.3 31.7 0.5
C10 A:AWE403 2.3 28.6 0.5
C12 A:AWE403 2.3 30.0 0.5
C8 A:AWE403 2.5 33.0 0.5
C11 A:AWE403 3.2 36.8 0.5
CG A:MET225 3.3 22.1 0.5
O A:MET221 3.3 14.7 1.0
C A:MET221 3.3 13.2 1.0
CG A:MET225 3.4 25.7 0.5
CB A:MET221 3.5 13.8 1.0
N A:LEU222 3.6 11.4 1.0
C9 A:AWE403 3.6 25.1 0.5
C7 A:AWE403 3.6 29.2 0.5
C7 A:AWE403 3.6 30.2 0.5
SD A:MET137 3.7 18.2 1.0
CA A:LEU222 3.8 11.9 1.0
CE A:MET221 3.9 20.6 1.0
C12 A:AWE403 3.9 33.0 0.5
CA A:MET221 4.0 10.8 1.0
C8 A:AWE403 4.1 26.8 0.5
CB A:MET225 4.1 17.8 0.5
CB A:MET225 4.2 20.4 0.5
F A:AWE403 4.3 40.8 0.5
CG A:MET137 4.4 15.6 1.0
SD A:MET225 4.6 27.0 0.5
O A:HOH703 4.6 55.4 1.0
CG A:MET221 4.7 17.6 1.0
CB A:LEU222 4.7 12.2 1.0
C4 A:AWE403 4.8 31.5 0.5
C4 A:AWE403 4.9 28.4 0.5
C A:LEU222 5.0 14.2 1.0

Fluorine binding site 3 out of 11 in 5oul

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Fluorine binding site 3 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F404

b:35.0
occ:0.50
 F A:AWE404 0.0 35.0 0.5
C11 A:AWE404 1.4 32.8 0.5
C9 A:AWE404 1.6 77.3 0.5
C10 A:AWE404 2.3 33.9 0.5
C12 A:AWE404 2.3 31.0 0.5
C8 A:AWE404 2.6 77.0 0.5
C10 A:AWE404 2.6 77.7 0.5
CD1 A:LEU298 3.2 18.1 1.0
CA A:PRO295 3.3 16.4 1.0
C9 A:AWE404 3.6 34.2 0.5
C7 A:AWE404 3.6 29.4 0.5
CG A:LEU298 3.7 18.1 1.0
C11 A:AWE404 3.8 77.9 0.5
N A:PRO295 3.9 15.6 1.0
C7 A:AWE404 3.9 76.7 0.5
CB A:LEU298 3.9 13.6 1.0
CB A:PRO295 4.0 19.7 1.0
O A:SER294 4.1 14.7 1.0
C8 A:AWE404 4.1 32.7 0.5
C A:SER294 4.2 16.6 1.0
CG A:PRO295 4.2 23.6 1.0
C12 A:AWE404 4.4 77.5 0.5
C A:PRO295 4.4 18.8 1.0
O A:PRO295 4.4 16.1 1.0
CD A:PRO295 4.6 18.6 1.0
C4 A:AWE404 4.9 24.4 0.5
F A:AWE404 4.9 77.9 0.5

Fluorine binding site 4 out of 11 in 5oul

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Fluorine binding site 4 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F404

b:77.9
occ:0.50
 F A:AWE404 0.0 77.9 0.5
C11 A:AWE404 1.4 77.9 0.5
C9 A:AWE404 1.4 34.2 0.5
C8 A:AWE404 2.1 32.7 0.5
C12 A:AWE404 2.3 77.5 0.5
C10 A:AWE404 2.3 77.7 0.5
C10 A:AWE404 2.6 33.9 0.5
CL A:AWE405 3.4 43.7 1.0
C7 A:AWE404 3.4 29.4 0.5
C9 A:AWE404 3.6 77.3 0.5
C7 A:AWE404 3.6 76.7 0.5
C11 A:AWE404 3.7 32.8 0.5
C12 A:AWE405 4.1 43.2 1.0
C12 A:AWE404 4.1 31.0 0.5
F A:AWE405 4.1 43.2 1.0
C8 A:AWE404 4.1 77.0 0.5
C11 A:AWE405 4.5 43.4 1.0
C4 A:AWE404 4.5 24.4 0.5
C5 A:AWE405 4.7 38.6 1.0
C4 A:AWE404 4.9 75.9 0.5
F A:AWE404 4.9 35.0 0.5
CL A:AWE404 5.0 32.0 0.5

Fluorine binding site 5 out of 11 in 5oul

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Fluorine binding site 5 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F405

b:43.2
occ:1.00
 F A:AWE405 0.0 43.2 1.0
C11 A:AWE405 1.4 43.4 1.0
C10 A:AWE405 2.3 43.0 1.0
C12 A:AWE405 2.4 43.2 1.0
C12 A:AWE404 3.2 77.5 0.5
C8 A:AWE404 3.5 32.7 0.5
C9 A:AWE405 3.6 43.5 1.0
C7 A:AWE405 3.6 41.9 1.0
C5 A:AWE404 3.7 25.3 0.5
CL A:AWE404 3.8 32.0 0.5
C4 A:AWE404 3.9 24.4 0.5
C4 A:AWE404 3.9 75.9 0.5
C7 A:AWE404 4.0 76.7 0.5
F A:AWE404 4.1 77.9 0.5
C8 A:AWE405 4.1 43.1 1.0
C6 A:AWE404 4.1 22.9 0.5
C11 A:AWE404 4.1 77.9 0.5
C7 A:AWE404 4.2 29.4 0.5
C3 A:AWE404 4.3 75.8 0.5
C5 A:AWE404 4.3 75.5 0.5
C3 A:AWE404 4.5 22.8 0.5
C9 A:AWE404 4.6 34.2 0.5
C1 A:AWE404 4.7 20.2 0.5
CL A:AWE404 4.8 75.3 0.5
C2 A:AWE404 4.8 18.8 0.5
C6 A:AWE404 4.8 75.2 0.5
C2 A:AWE404 4.8 75.6 0.5
C4 A:AWE405 4.9 40.0 1.0
CL A:AWE405 4.9 43.7 1.0

Fluorine binding site 6 out of 11 in 5oul

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Fluorine binding site 6 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F406

b:45.1
occ:1.00
 F A:AWE406 0.0 45.1 1.0
C11 A:AWE406 1.4 41.7 1.0
C12 A:AWE406 2.3 39.5 1.0
C10 A:AWE406 2.3 42.2 1.0
CD A:LYS71 3.6 34.5 1.0
C9 A:AWE406 3.6 40.2 1.0
C7 A:AWE406 3.6 40.8 1.0
CE A:LYS71 3.9 47.6 1.0
CG A:LYS71 3.9 26.5 1.0
C8 A:AWE406 4.1 38.7 1.0
NZ A:LYS71 4.3 44.9 1.0
CB A:LYS71 4.3 21.5 1.0
CD A:PRO72 4.4 37.1 1.0
C4 A:AWE406 4.9 42.9 1.0

Fluorine binding site 7 out of 11 in 5oul

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Fluorine binding site 7 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F407

b:37.9
occ:1.00
 F A:AWE407 0.0 37.9 1.0
C11 A:AWE407 1.4 36.3 1.0
C12 A:AWE407 2.3 37.0 1.0
C10 A:AWE407 2.4 31.2 1.0
CB A:VAL116 3.5 27.9 1.0
CG2 A:VAL116 3.6 27.8 1.0
C9 A:AWE407 3.6 33.3 1.0
C7 A:AWE407 3.6 39.0 1.0
CG A:MET163 3.7 22.1 1.0
N A:VAL116 3.8 24.5 1.0
CD1 A:ILE95 3.8 17.0 1.0
C8 A:AWE407 4.1 36.5 1.0
CA A:VAL116 4.1 24.2 1.0
O A:GLU114 4.2 27.0 1.0
CG2 A:ILE174 4.2 15.7 1.0
CB A:MET163 4.2 18.6 1.0
O A:VAL116 4.3 29.8 1.0
CG2 A:VAL66 4.4 20.4 1.0
F3 A:TFA409 4.5 34.7 1.0
SD A:MET163 4.6 27.5 1.0
C A:HIS115 4.7 27.5 1.0
C A:VAL116 4.7 29.1 1.0
CG1 A:VAL116 4.7 28.0 1.0
CG1 A:ILE95 4.7 15.4 1.0
C4 A:AWE407 4.9 45.1 1.0
CB A:VAL66 5.0 20.4 1.0
CA A:HIS115 5.0 24.1 1.0

Fluorine binding site 8 out of 11 in 5oul

Go back to Fluorine Binding Sites List in 5oul
Fluorine binding site 8 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F408

b:96.5
occ:1.00
 F A:AWE408 0.0 96.5 1.0
C11 A:AWE408 1.4 97.0 1.0
C10 A:AWE408 2.3 97.4 1.0
C12 A:AWE408 2.3 97.2 1.0
OD1 A:ASN161 2.7 17.8 1.0
O A:HOH663 3.1 44.6 1.0
O A:HIS160 3.2 20.1 1.0
O A:HOH750 3.3 43.0 1.0
CD1 A:ILE174 3.6 16.1 1.0
C9 A:AWE408 3.6 97.3 1.0
C7 A:AWE408 3.6 97.3 1.0
CG A:ASN161 3.9 21.2 1.0
C A:HIS160 4.1 19.1 1.0
OD2 A:ASP175 4.1 36.1 1.0
C8 A:AWE408 4.1 97.4 1.0
CB A:ASP175 4.3 16.9 1.0
CA A:ASN161 4.5 13.2 1.0
CG1 A:ILE174 4.5 14.8 1.0
N A:ASN161 4.6 13.2 1.0
CB A:HIS160 4.6 21.4 1.0
CG A:ASP175 4.7 29.1 1.0
ND2 A:ASN161 4.8 16.1 1.0
CB A:ASN161 4.8 13.8 1.0
CL A:AWE408 4.8 98.2 1.0
C4 A:AWE408 4.9 97.9 1.0
CA A:HIS160 5.0 19.0 1.0

Fluorine binding site 9 out of 11 in 5oul

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Fluorine binding site 9 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:38.2
occ:1.00
 F1 A:TFA409 0.0 38.2 1.0
C2 A:TFA409 1.3 33.6 1.0
F2 A:TFA409 2.1 30.4 1.0
F3 A:TFA409 2.2 34.7 1.0
C1 A:TFA409 2.4 26.8 1.0
O A:TFA409 2.6 29.6 1.0
OXT A:TFA409 3.2 22.9 1.0
C9 A:AWE407 3.3 33.3 1.0
C10 A:AWE407 3.4 31.2 1.0
CD1 A:ILE174 3.5 16.1 1.0
O A:HOH663 3.8 44.6 1.0
O A:HOH750 4.1 43.0 1.0
CB A:ILE174 4.3 15.0 1.0
CG1 A:ILE174 4.5 14.8 1.0
CG2 A:VAL53 4.5 21.0 1.0
C8 A:AWE407 4.5 36.5 1.0
CG1 A:VAL53 4.7 21.9 1.0
CG1 A:VAL66 4.7 20.1 1.0
C11 A:AWE407 4.7 36.3 1.0
CG2 A:ILE174 4.8 15.7 1.0
N A:ASP175 4.8 14.0 1.0

Fluorine binding site 10 out of 11 in 5oul

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Fluorine binding site 10 out of 11 in the The Crystal Structure of CK2ALPHA in Complex with Compound 9


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of The Crystal Structure of CK2ALPHA in Complex with Compound 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:30.4
occ:1.00
 F2 A:TFA409 0.0 30.4 1.0
C2 A:TFA409 1.3 33.6 1.0
F1 A:TFA409 2.1 38.2 1.0
F3 A:TFA409 2.2 34.7 1.0
C1 A:TFA409 2.4 26.8 1.0
O A:TFA409 2.9 29.6 1.0
CE2 A:PHE113 3.2 16.5 1.0
CD2 A:PHE113 3.3 14.4 1.0
OXT A:TFA409 3.3 22.9 1.0
CB A:LYS68 3.5 14.7 1.0
CD A:LYS68 3.8 18.4 1.0
CG1 A:VAL66 3.9 20.1 1.0
CG A:LYS68 4.1 16.2 1.0
CZ A:PHE113 4.1 15.3 1.0
CG2 A:VAL53 4.3 21.0 1.0
CG A:PHE113 4.3 14.6 1.0
C10 A:AWE407 4.4 31.2 1.0
C9 A:AWE407 4.4 33.3 1.0
CG1 A:VAL53 4.5 21.9 1.0
CA A:LYS68 4.6 13.5 1.0
CE A:LYS68 4.7 30.2 1.0
N A:LYS68 4.8 13.2 1.0
NZ A:LYS68 4.8 25.7 1.0
O A:HOH663 4.9 44.6 1.0
CE1 A:PHE113 5.0 15.5 1.0

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: Thu Aug 1 12:36:13 2024

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