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Fluorine in PDB 2fpt: Dual Binding Mode of A Novel Series of Dhodh Inhibitors

Enzymatic activity of Dual Binding Mode of A Novel Series of Dhodh Inhibitors

All present enzymatic activity of Dual Binding Mode of A Novel Series of Dhodh Inhibitors:
1.3.3.1;

Protein crystallography data

The structure of Dual Binding Mode of A Novel Series of Dhodh Inhibitors, PDB code: 2fpt was solved by R.Baumgartner, M.Walloschek, M.Kralik, A.Gotschlich, S.Tasler, J.Leban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 11.97 / 2.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.651, 90.651, 123.072, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors (pdb code 2fpt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors, PDB code: 2fpt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 2fpt

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Fluorine binding site 1 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:23.4
occ:0.50
 F10 A:ILB405 0.0 23.4 0.5
F14 A:ILB405 0.1 22.1 0.5
C9 A:ILB405 1.3 23.3 0.5
C13 A:ILB405 1.3 21.5 0.5
C15 A:ILB405 2.3 22.4 0.5
C8 A:ILB405 2.4 24.2 0.5
C11 A:ILB405 2.4 24.9 0.5
C11 A:ILB405 2.5 23.1 0.5
N12 A:ILB405 2.8 23.5 0.5
N12 A:ILB405 3.0 22.0 0.5
O18 A:ILB405 3.2 29.7 0.5
C16 A:ILB405 3.3 28.3 0.5
CG A:LEU359 3.4 19.7 1.0
O24 A:ILB405 3.5 28.2 0.5
CA A:THR360 3.6 18.3 1.0
C6 A:ILB405 3.7 24.8 0.5
CE1 A:PHE98 3.7 20.1 1.0
N A:THR360 3.7 17.5 1.0
O A:LEU359 3.7 16.0 1.0
C13 A:ILB405 3.7 26.4 0.5
CG2 A:THR360 3.7 14.0 1.0
C6 A:ILB405 3.7 26.7 0.5
C9 A:ILB405 3.8 23.9 0.5
C A:LEU359 3.8 17.1 1.0
CD2 A:LEU359 3.8 19.8 1.0
CB A:LEU359 4.1 19.0 1.0
CD1 A:PHE98 4.2 20.6 1.0
CB A:THR360 4.2 17.8 1.0
C8 A:ILB405 4.2 23.8 0.5
C16 A:ILB405 4.2 27.2 0.5
C15 A:ILB405 4.2 26.3 0.5
CB A:ALA59 4.4 21.5 1.0
C17 A:ILB405 4.5 27.5 0.5
C23 A:ILB405 4.5 26.6 0.5
CD1 A:LEU359 4.6 18.6 1.0
CZ A:PHE98 4.6 21.7 1.0
CA A:LEU359 4.6 17.9 1.0
F14 A:ILB405 4.8 28.1 0.5
F10 A:ILB405 4.9 22.4 0.5
C5 A:ILB405 4.9 25.3 0.5
C5 A:ILB405 4.9 27.7 0.5
C A:THR360 4.9 19.7 1.0
CE2 A:TYR356 4.9 15.0 1.0
O18 A:ILB405 4.9 30.8 0.5

Fluorine binding site 2 out of 10 in 2fpt

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Fluorine binding site 2 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:22.4
occ:0.50
 F10 A:ILB405 0.0 22.4 0.5
F14 A:ILB405 0.1 28.1 0.5
C13 A:ILB405 1.3 26.4 0.5
C9 A:ILB405 1.3 23.9 0.5
C15 A:ILB405 2.3 26.3 0.5
C11 A:ILB405 2.4 23.1 0.5
C8 A:ILB405 2.4 23.8 0.5
C11 A:ILB405 2.4 24.9 0.5
N12 A:ILB405 2.7 22.0 0.5
O18 A:ILB405 2.8 30.8 0.5
N12 A:ILB405 2.9 23.5 0.5
C16 A:ILB405 3.0 27.2 0.5
O A:ALA55 3.2 22.8 1.0
CB A:ALA55 3.3 22.4 1.0
O24 A:ILB405 3.4 35.1 0.5
C A:ALA55 3.5 23.0 1.0
CD2 A:LEU46 3.7 40.4 1.0
C13 A:ILB405 3.7 21.5 0.5
C6 A:ILB405 3.7 26.7 0.5
C6 A:ILB405 3.7 24.8 0.5
C9 A:ILB405 3.8 23.3 0.5
CA A:ALA55 3.8 23.5 1.0
C16 A:ILB405 4.0 28.3 0.5
C15 A:ILB405 4.2 22.4 0.5
C8 A:ILB405 4.2 24.2 0.5
CB A:ALA59 4.3 21.5 1.0
N A:HIS56 4.3 22.2 1.0
C17 A:ILB405 4.3 24.6 0.5
CE A:MET43 4.3 21.1 1.0
CG A:LEU46 4.4 40.3 1.0
O18 A:ILB405 4.5 29.7 0.5
C23 A:ILB405 4.5 31.4 0.5
F14 A:ILB405 4.8 22.1 0.5
CA A:HIS56 4.8 23.8 1.0
O24 A:ILB405 4.9 28.2 0.5
F10 A:ILB405 4.9 23.4 0.5
C5 A:ILB405 4.9 27.7 0.5
C5 A:ILB405 4.9 25.3 0.5
C17 A:ILB405 5.0 27.5 0.5

Fluorine binding site 3 out of 10 in 2fpt

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Fluorine binding site 3 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:28.1
occ:0.50
 F14 A:ILB405 0.0 28.1 0.5
F10 A:ILB405 0.1 22.4 0.5
C13 A:ILB405 1.3 26.4 0.5
C9 A:ILB405 1.3 23.9 0.5
C11 A:ILB405 2.4 23.1 0.5
C15 A:ILB405 2.4 26.3 0.5
C11 A:ILB405 2.4 24.9 0.5
C8 A:ILB405 2.4 23.8 0.5
N12 A:ILB405 2.7 22.0 0.5
O18 A:ILB405 2.8 30.8 0.5
N12 A:ILB405 2.9 23.5 0.5
C16 A:ILB405 3.0 27.2 0.5
O A:ALA55 3.2 22.8 1.0
CB A:ALA55 3.3 22.4 1.0
O24 A:ILB405 3.4 35.1 0.5
C A:ALA55 3.5 23.0 1.0
C13 A:ILB405 3.7 21.5 0.5
CD2 A:LEU46 3.7 40.4 1.0
C6 A:ILB405 3.7 26.7 0.5
C6 A:ILB405 3.8 24.8 0.5
C9 A:ILB405 3.8 23.3 0.5
CA A:ALA55 3.8 23.5 1.0
C16 A:ILB405 3.9 28.3 0.5
C15 A:ILB405 4.2 22.4 0.5
C8 A:ILB405 4.3 24.2 0.5
N A:HIS56 4.3 22.2 1.0
CB A:ALA59 4.3 21.5 1.0
C17 A:ILB405 4.3 24.6 0.5
CE A:MET43 4.4 21.1 1.0
CG A:LEU46 4.4 40.3 1.0
O18 A:ILB405 4.5 29.7 0.5
C23 A:ILB405 4.5 31.4 0.5
F14 A:ILB405 4.8 22.1 0.5
CA A:HIS56 4.8 23.8 1.0
O24 A:ILB405 4.8 28.2 0.5
F10 A:ILB405 4.8 23.4 0.5
C17 A:ILB405 4.9 27.5 0.5
C5 A:ILB405 4.9 27.7 0.5
C5 A:ILB405 4.9 25.3 0.5

Fluorine binding site 4 out of 10 in 2fpt

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Fluorine binding site 4 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:22.1
occ:0.50
 F14 A:ILB405 0.0 22.1 0.5
F10 A:ILB405 0.1 23.4 0.5
C13 A:ILB405 1.3 21.5 0.5
C9 A:ILB405 1.3 23.3 0.5
C11 A:ILB405 2.4 24.9 0.5
C15 A:ILB405 2.4 22.4 0.5
C11 A:ILB405 2.4 23.1 0.5
C8 A:ILB405 2.4 24.2 0.5
N12 A:ILB405 2.7 23.5 0.5
N12 A:ILB405 2.9 22.0 0.5
O18 A:ILB405 3.2 29.7 0.5
C16 A:ILB405 3.2 28.3 0.5
O24 A:ILB405 3.4 28.2 0.5
CG A:LEU359 3.5 19.7 1.0
CA A:THR360 3.5 18.3 1.0
CG2 A:THR360 3.6 14.0 1.0
N A:THR360 3.6 17.5 1.0
O A:LEU359 3.7 16.0 1.0
C13 A:ILB405 3.7 26.4 0.5
C A:LEU359 3.7 17.1 1.0
C9 A:ILB405 3.7 23.9 0.5
C6 A:ILB405 3.7 24.8 0.5
C6 A:ILB405 3.8 26.7 0.5
CE1 A:PHE98 3.8 20.1 1.0
CD2 A:LEU359 3.9 19.8 1.0
CB A:THR360 4.0 17.8 1.0
C16 A:ILB405 4.1 27.2 0.5
CB A:LEU359 4.1 19.0 1.0
C8 A:ILB405 4.2 23.8 0.5
C15 A:ILB405 4.2 26.3 0.5
CD1 A:PHE98 4.3 20.6 1.0
C17 A:ILB405 4.4 27.5 0.5
C23 A:ILB405 4.4 26.6 0.5
CB A:ALA59 4.4 21.5 1.0
CA A:LEU359 4.6 17.9 1.0
CD1 A:LEU359 4.6 18.6 1.0
CZ A:PHE98 4.7 21.7 1.0
F14 A:ILB405 4.8 28.1 0.5
F10 A:ILB405 4.8 22.4 0.5
C A:THR360 4.8 19.7 1.0
O18 A:ILB405 4.8 30.8 0.5
CE2 A:TYR356 4.9 15.0 1.0
C5 A:ILB405 4.9 25.3 0.5
C17 A:ILB405 5.0 24.6 0.5
C5 A:ILB405 5.0 27.7 0.5

Fluorine binding site 5 out of 10 in 2fpt

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Fluorine binding site 5 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:45.1
occ:0.50
 F28 A:ILB405 0.0 45.1 0.5
F28 A:ILB405 0.3 37.3 0.5
C27 A:ILB405 1.3 42.6 0.5
C27 A:ILB405 1.4 36.5 0.5
F29 A:ILB405 2.0 36.1 0.5
F30 A:ILB405 2.1 44.0 0.5
F29 A:ILB405 2.2 43.8 0.5
F30 A:ILB405 2.3 36.9 0.5
O26 A:ILB405 2.4 39.7 0.5
O26 A:ILB405 2.4 34.4 0.5
C3 A:ILB405 2.9 32.8 0.5
C3 A:ILB405 3.0 29.1 0.5
C4 A:ILB405 3.3 30.8 0.5
C4 A:ILB405 3.4 27.7 0.5
CD2 A:LEU42 3.8 35.1 1.0
C2 A:ILB405 3.9 31.3 0.5
C2 A:ILB405 4.0 27.5 0.5
CD2 A:PHE62 4.2 39.7 1.0
CE2 A:PHE62 4.3 41.0 1.0
CD1 A:LEU42 4.4 34.8 1.0
CD2 A:LEU46 4.5 40.4 1.0
C5 A:ILB405 4.5 27.7 0.5
C5 A:ILB405 4.6 25.3 0.5
CG A:LEU42 4.7 35.2 1.0
C1 A:ILB405 4.9 30.6 0.5
CG A:PHE62 5.0 35.9 1.0

Fluorine binding site 6 out of 10 in 2fpt

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Fluorine binding site 6 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:37.3
occ:0.50
 F28 A:ILB405 0.0 37.3 0.5
F28 A:ILB405 0.3 45.1 0.5
C27 A:ILB405 1.3 36.5 0.5
C27 A:ILB405 1.4 42.6 0.5
F30 A:ILB405 2.0 44.0 0.5
F29 A:ILB405 2.2 36.1 0.5
F30 A:ILB405 2.2 36.9 0.5
O26 A:ILB405 2.3 34.4 0.5
O26 A:ILB405 2.3 39.7 0.5
F29 A:ILB405 2.4 43.8 0.5
C3 A:ILB405 2.7 32.8 0.5
C3 A:ILB405 2.7 29.1 0.5
C4 A:ILB405 3.1 30.8 0.5
C4 A:ILB405 3.2 27.7 0.5
C2 A:ILB405 3.6 31.3 0.5
C2 A:ILB405 3.7 27.5 0.5
CD2 A:PHE62 4.0 39.7 1.0
CD2 A:LEU42 4.0 35.1 1.0
CE2 A:PHE62 4.2 41.0 1.0
C5 A:ILB405 4.3 27.7 0.5
C5 A:ILB405 4.4 25.3 0.5
CD2 A:LEU46 4.5 40.4 1.0
C1 A:ILB405 4.6 30.6 0.5
CD1 A:LEU42 4.7 34.8 1.0
C1 A:ILB405 4.7 27.7 0.5
CG A:PHE62 4.7 35.9 1.0
C7 A:ILB405 4.9 27.3 0.5
CG A:LEU42 5.0 35.2 1.0
C7 A:ILB405 5.0 25.1 0.5

Fluorine binding site 7 out of 10 in 2fpt

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Fluorine binding site 7 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:43.8
occ:0.50
 F29 A:ILB405 0.0 43.8 0.5
F29 A:ILB405 0.2 36.1 0.5
C27 A:ILB405 1.3 42.6 0.5
C27 A:ILB405 1.5 36.5 0.5
F30 A:ILB405 2.1 44.0 0.5
F28 A:ILB405 2.2 45.1 0.5
O26 A:ILB405 2.3 39.7 0.5
F30 A:ILB405 2.3 36.9 0.5
F28 A:ILB405 2.4 37.3 0.5
O26 A:ILB405 2.4 34.4 0.5
CD1 A:LEU42 3.2 34.8 1.0
C3 A:ILB405 3.5 32.8 0.5
C3 A:ILB405 3.7 29.1 0.5
OH A:TYR38 3.7 30.9 1.0
CE2 A:TYR38 3.9 27.4 1.0
CD2 A:LEU42 3.9 35.1 1.0
CG A:LEU42 4.1 35.2 1.0
O A:HOH582 4.2 55.3 1.0
CZ A:TYR38 4.2 29.9 1.0
CE A:MET30 4.2 80.7 1.0
SD A:MET30 4.3 80.9 1.0
C2 A:ILB405 4.4 31.3 0.5
C4 A:ILB405 4.5 30.8 0.5
C2 A:ILB405 4.5 27.5 0.5
C4 A:ILB405 4.6 27.7 0.5
CD2 A:TYR38 5.0 27.3 1.0

Fluorine binding site 8 out of 10 in 2fpt

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Fluorine binding site 8 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:36.1
occ:0.50
 F29 A:ILB405 0.0 36.1 0.5
F29 A:ILB405 0.2 43.8 0.5
C27 A:ILB405 1.1 42.6 0.5
C27 A:ILB405 1.3 36.5 0.5
F28 A:ILB405 2.0 45.1 0.5
F30 A:ILB405 2.0 44.0 0.5
O26 A:ILB405 2.1 39.7 0.5
F30 A:ILB405 2.1 36.9 0.5
F28 A:ILB405 2.2 37.3 0.5
O26 A:ILB405 2.2 34.4 0.5
CD1 A:LEU42 3.3 34.8 1.0
C3 A:ILB405 3.3 32.8 0.5
C3 A:ILB405 3.5 29.1 0.5
OH A:TYR38 3.8 30.9 1.0
CD2 A:LEU42 3.9 35.1 1.0
CE2 A:TYR38 3.9 27.4 1.0
CG A:LEU42 4.2 35.2 1.0
C2 A:ILB405 4.2 31.3 0.5
CZ A:TYR38 4.2 29.9 1.0
C4 A:ILB405 4.3 30.8 0.5
O A:HOH582 4.3 55.3 1.0
C2 A:ILB405 4.3 27.5 0.5
C4 A:ILB405 4.4 27.7 0.5
CE A:MET30 4.4 80.7 1.0
SD A:MET30 4.5 80.9 1.0
CD2 A:TYR38 5.0 27.3 1.0
CD2 A:PHE62 5.0 39.7 1.0

Fluorine binding site 9 out of 10 in 2fpt

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Fluorine binding site 9 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:44.0
occ:0.50
 F30 A:ILB405 0.0 44.0 0.5
F30 A:ILB405 0.2 36.9 0.5
C27 A:ILB405 1.2 36.5 0.5
C27 A:ILB405 1.3 42.6 0.5
F29 A:ILB405 2.0 36.1 0.5
F28 A:ILB405 2.0 37.3 0.5
F28 A:ILB405 2.1 45.1 0.5
F29 A:ILB405 2.1 43.8 0.5
O26 A:ILB405 2.3 34.4 0.5
O26 A:ILB405 2.3 39.7 0.5
C3 A:ILB405 2.9 32.8 0.5
C3 A:ILB405 2.9 29.1 0.5
C2 A:ILB405 3.1 31.3 0.5
C2 A:ILB405 3.1 27.5 0.5
CD2 A:PHE62 3.2 39.7 1.0
O A:LEU67 3.4 36.5 1.0
CE2 A:PHE62 3.7 41.0 1.0
C4 A:ILB405 4.0 30.8 0.5
C4 A:ILB405 4.1 27.7 0.5
CG A:PHE62 4.2 35.9 1.0
C1 A:ILB405 4.3 30.6 0.5
C1 A:ILB405 4.4 27.7 0.5
C A:LEU67 4.6 37.1 1.0
CB A:PHE62 4.6 31.6 1.0
O A:HOH582 4.7 55.3 1.0
OH A:TYR38 4.8 30.9 1.0
CB A:LEU67 4.8 39.3 1.0
CZ A:PHE62 5.0 39.9 1.0

Fluorine binding site 10 out of 10 in 2fpt

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Fluorine binding site 10 out of 10 in the Dual Binding Mode of A Novel Series of Dhodh Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Dual Binding Mode of A Novel Series of Dhodh Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:36.9
occ:0.50
 F30 A:ILB405 0.0 36.9 0.5
F30 A:ILB405 0.2 44.0 0.5
C27 A:ILB405 1.3 36.5 0.5
C27 A:ILB405 1.4 42.6 0.5
F29 A:ILB405 2.1 36.1 0.5
F28 A:ILB405 2.2 37.3 0.5
F29 A:ILB405 2.3 43.8 0.5
F28 A:ILB405 2.3 45.1 0.5
O26 A:ILB405 2.3 34.4 0.5
O26 A:ILB405 2.3 39.7 0.5
C3 A:ILB405 2.8 32.8 0.5
C3 A:ILB405 2.8 29.1 0.5
C2 A:ILB405 3.0 31.3 0.5
C2 A:ILB405 3.0 27.5 0.5
CD2 A:PHE62 3.2 39.7 1.0
O A:LEU67 3.3 36.5 1.0
CE2 A:PHE62 3.8 41.0 1.0
C4 A:ILB405 4.0 30.8 0.5
C4 A:ILB405 4.0 27.7 0.5
C1 A:ILB405 4.2 30.6 0.5
CG A:PHE62 4.2 35.9 1.0
C1 A:ILB405 4.3 27.7 0.5
C A:LEU67 4.4 37.1 1.0
CB A:PHE62 4.5 31.6 1.0
O A:HOH582 4.7 55.3 1.0
CB A:LEU67 4.7 39.3 1.0
OH A:TYR38 4.8 30.9 1.0

Reference:

R.Baumgartner, M.Walloschek, M.Kralik, A.Gotschlich, S.Tasler, J.Mies, J.Leban. Dual Binding Mode of A Novel Series of Dhodh Inhibitors. J.Med.Chem. V. 49 1239 2006.
ISSN: ISSN 0022-2623
PubMed: 16480261
DOI: 10.1021/JM0506975
Page generated: Sun Dec 13 11:36:05 2020

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