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Fluorine in PDB 8v39: Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520

Enzymatic activity of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520

All present enzymatic activity of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520, PDB code: 8v39 was solved by A.H.Chan, M.Ashraf, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.78 / 2.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.96, 115.96, 180.5, 90, 90, 120
R / Rfree (%) 26.6 / 31.2

Other elements in 8v39:

The structure of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 (pdb code 8v39). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520, PDB code: 8v39:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 8v39

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Fluorine binding site 1 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:19.9
occ:1.00
 F1 A:Y8N203 0.0 19.9 1.0
C8 A:Y8N203 1.3 18.2 1.0
C4 A:Y8N203 2.4 18.7 1.0
C7 A:Y8N203 2.4 17.1 1.0
N2 A:Y8N203 2.7 18.0 1.0
C11 A:Y8N203 2.8 15.8 1.0
NE2 A:HIS95 3.0 19.5 1.0
C16 A:Y8N203 3.3 16.0 1.0
CG A:GLN99 3.4 18.5 1.0
C12 A:Y8N203 3.4 16.4 1.0
CD2 A:HIS95 3.6 17.8 1.0
C6 A:Y8N203 3.6 17.0 1.0
C3 A:Y8N203 3.7 18.8 1.0
C34 A:Y8N203 3.8 16.3 1.0
OH A:TYR64 3.8 19.0 1.0
C33 A:Y8N203 3.8 16.8 1.0
CB A:GLN99 3.8 16.1 1.0
CE1 A:HIS95 3.9 19.4 1.0
CD1 A:TYR96 3.9 16.6 1.0
C1 A:Y8N203 4.0 19.2 1.0
CE1 A:TYR96 4.0 19.1 1.0
C5 A:Y8N203 4.1 18.4 1.0
N7 A:Y8N203 4.2 18.1 1.0
C15 A:Y8N203 4.3 13.0 1.0
CE1 A:TYR64 4.4 17.1 1.0
C13 A:Y8N203 4.4 13.5 1.0
CZ A:TYR64 4.5 19.0 1.0
CA A:TYR96 4.6 19.1 1.0
CG A:TYR96 4.6 19.4 1.0
CD A:GLN99 4.6 17.1 1.0
CG A:HIS95 4.7 20.6 1.0
C14 A:Y8N203 4.7 14.6 1.0
O1 A:Y8N203 4.8 19.7 1.0
ND1 A:HIS95 4.8 17.1 1.0
C2 A:Y8N203 4.8 19.1 1.0
O A:HIS95 4.8 18.4 1.0
CZ A:TYR96 4.9 20.8 1.0
C32 A:Y8N203 4.9 13.8 1.0
N1 A:Y8N203 4.9 21.0 1.0
C35 A:Y8N203 4.9 19.2 1.0

Fluorine binding site 2 out of 18 in 8v39

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Fluorine binding site 2 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:24.0
occ:1.00
 F2 A:Y8N203 0.0 24.0 1.0
C22 A:Y8N203 1.4 21.1 1.0
C23 A:Y8N203 2.4 19.4 1.0
C21 A:Y8N203 2.4 19.4 1.0
N5 A:Y8N203 2.9 18.7 1.0
C10 A:Y8N203 3.0 20.1 1.0
C26 A:Y8N203 3.2 20.6 1.0
C24 A:Y8N203 3.3 21.3 1.0
O A:HOH373 3.6 23.8 1.0
C25 A:Y8N203 3.9 18.6 1.0
O A:HOH385 3.9 32.0 1.0
C9 A:Y8N203 4.5 17.5 1.0
OD1 A:ASP92 4.8 28.2 1.0
O1 A:Y8N203 4.8 19.7 1.0

Fluorine binding site 3 out of 18 in 8v39

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Fluorine binding site 3 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:20.4
occ:1.00
 F3 A:Y8N203 0.0 20.4 1.0
C14 A:Y8N203 1.3 14.6 1.0
C15 A:Y8N203 2.3 13.0 1.0
C13 A:Y8N203 2.4 13.5 1.0
S1 A:Y8N203 3.0 13.5 1.0
CG2 A:VAL103 3.2 17.7 1.0
O A:GLN99 3.5 18.0 1.0
CB A:MET72 3.6 20.0 1.0
CA A:ILE100 3.6 19.3 1.0
C12 A:Y8N203 3.6 16.4 1.0
C16 A:Y8N203 3.6 16.0 1.0
C A:GLN99 3.6 16.8 1.0
N A:ILE100 3.6 17.5 1.0
CG1 A:ILE100 3.9 20.2 1.0
CG A:MET72 4.0 19.9 1.0
C11 A:Y8N203 4.1 15.8 1.0
CB A:GLN99 4.2 16.1 1.0
CG1 A:VAL103 4.3 18.8 1.0
CB A:ILE100 4.4 20.2 1.0
CB A:VAL103 4.4 23.4 1.0
CE2 A:PHE78 4.5 18.3 1.0
C32 A:Y8N203 4.5 13.8 1.0
CA A:GLN99 4.6 17.3 1.0
C33 A:Y8N203 4.6 16.8 1.0
C A:ILE100 4.7 19.3 1.0
CZ A:PHE78 4.8 20.6 1.0
O A:ILE100 4.8 19.2 1.0
CA A:MET72 4.9 20.1 1.0
SD A:MET72 4.9 31.2 1.0

Fluorine binding site 4 out of 18 in 8v39

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Fluorine binding site 4 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:19.5
occ:1.00
 F4 A:Y8N203 0.0 19.5 1.0
C35 A:Y8N203 1.3 19.2 1.0
F5 A:Y8N203 2.1 20.1 1.0
F6 A:Y8N203 2.1 20.7 1.0
C6 A:Y8N203 2.3 17.0 1.0
C7 A:Y8N203 3.0 17.1 1.0
C11 A:Y8N203 3.0 15.8 1.0
C12 A:Y8N203 3.1 16.4 1.0
CG1 A:VAL9 3.3 18.5 1.0
C5 A:Y8N203 3.4 18.4 1.0
O A:HOH360 3.7 17.2 1.0
CG2 A:THR58 3.7 17.0 1.0
OG1 A:THR58 3.7 19.8 1.0
CB A:VAL9 3.8 16.6 1.0
CB A:THR58 3.9 21.5 1.0
C16 A:Y8N203 4.0 16.0 1.0
SD A:MET72 4.0 31.2 1.0
C13 A:Y8N203 4.0 13.5 1.0
CE A:MET72 4.2 17.8 1.0
C8 A:Y8N203 4.3 18.2 1.0
C3 A:Y8N203 4.6 18.8 1.0
CA A:VAL9 4.6 18.3 1.0
C15 A:Y8N203 4.8 13.0 1.0
C14 A:Y8N203 4.8 14.6 1.0
CE1 A:TYR96 4.8 19.1 1.0
NH2 A:ARG68 4.8 20.1 1.0
C33 A:Y8N203 4.9 16.8 1.0
CG A:MET72 4.9 19.9 1.0
C4 A:Y8N203 4.9 18.7 1.0
CD1 A:TYR96 5.0 16.6 1.0
C34 A:Y8N203 5.0 16.3 1.0
O A:HOH328 5.0 18.0 1.0
CG2 A:VAL9 5.0 18.5 1.0

Fluorine binding site 5 out of 18 in 8v39

Go back to Fluorine Binding Sites List in 8v39
Fluorine binding site 5 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:20.1
occ:1.00
 F5 A:Y8N203 0.0 20.1 1.0
C35 A:Y8N203 1.3 19.2 1.0
F4 A:Y8N203 2.1 19.5 1.0
F6 A:Y8N203 2.1 20.7 1.0
C6 A:Y8N203 2.4 17.0 1.0
C11 A:Y8N203 2.9 15.8 1.0
C7 A:Y8N203 3.0 17.1 1.0
C16 A:Y8N203 3.2 16.0 1.0
O A:HOH328 3.3 18.0 1.0
CE A:MET72 3.4 17.8 1.0
C34 A:Y8N203 3.4 16.3 1.0
C5 A:Y8N203 3.5 18.4 1.0
C33 A:Y8N203 3.5 16.8 1.0
NH2 A:ARG68 3.6 20.1 1.0
SD A:MET72 3.6 31.2 1.0
NE A:ARG68 3.7 18.7 1.0
C12 A:Y8N203 3.7 16.4 1.0
N7 A:Y8N203 3.8 18.1 1.0
CG A:MET72 3.9 19.9 1.0
CZ A:ARG68 4.0 22.4 1.0
C15 A:Y8N203 4.1 13.0 1.0
C8 A:Y8N203 4.3 18.2 1.0
C32 A:Y8N203 4.4 13.8 1.0
C13 A:Y8N203 4.5 13.5 1.0
CG2 A:THR58 4.6 17.0 1.0
C14 A:Y8N203 4.6 14.6 1.0
C3 A:Y8N203 4.7 18.8 1.0
CD A:ARG68 4.7 20.1 1.0
CG A:ARG68 4.7 22.2 1.0
CB A:THR58 4.8 21.5 1.0
C4 A:Y8N203 5.0 18.7 1.0

Fluorine binding site 6 out of 18 in 8v39

Go back to Fluorine Binding Sites List in 8v39
Fluorine binding site 6 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:20.7
occ:1.00
 F6 A:Y8N203 0.0 20.7 1.0
C35 A:Y8N203 1.3 19.2 1.0
F5 A:Y8N203 2.1 20.1 1.0
F4 A:Y8N203 2.1 19.5 1.0
C6 A:Y8N203 2.4 17.0 1.0
C5 A:Y8N203 2.7 18.4 1.0
NH2 A:ARG68 3.2 20.1 1.0
CB A:THR58 3.4 21.5 1.0
O A:HOH328 3.4 18.0 1.0
OG1 A:THR58 3.6 19.8 1.0
O A:HOH360 3.6 17.2 1.0
C7 A:Y8N203 3.6 17.1 1.0
CG2 A:THR58 3.9 17.0 1.0
C28 A:Y8N203 4.0 23.2 1.0
C3 A:Y8N203 4.1 18.8 1.0
CZ A:ARG68 4.2 22.4 1.0
C11 A:Y8N203 4.3 15.8 1.0
CE A:MET72 4.4 17.8 1.0
NE A:ARG68 4.4 18.7 1.0
C20 A:Y8N203 4.6 22.4 1.0
CA A:THR58 4.7 19.2 1.0
N7 A:Y8N203 4.7 18.1 1.0
OE1 A:GLU37 4.8 23.6 1.0
C8 A:Y8N203 4.8 18.2 1.0
C34 A:Y8N203 4.8 16.3 1.0
C12 A:Y8N203 4.9 16.4 1.0
N A:ALA59 4.9 22.3 1.0
C A:THR58 4.9 20.7 1.0
C19 A:Y8N203 5.0 26.5 1.0
C4 A:Y8N203 5.0 18.7 1.0
SD A:MET72 5.0 31.2 1.0
C16 A:Y8N203 5.0 16.0 1.0

Fluorine binding site 7 out of 18 in 8v39

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Fluorine binding site 7 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:31.6
occ:1.00
 F1 B:Y8N203 0.0 31.6 1.0
C8 B:Y8N203 1.3 30.6 1.0
C7 B:Y8N203 2.3 27.1 1.0
C4 B:Y8N203 2.4 31.4 1.0
C11 B:Y8N203 2.7 31.2 1.0
N2 B:Y8N203 2.7 31.2 1.0
NE2 B:HIS95 3.0 34.0 1.0
C16 B:Y8N203 3.2 27.8 1.0
C12 B:Y8N203 3.4 29.7 1.0
CG B:GLN99 3.4 32.2 1.0
CD2 B:HIS95 3.6 32.9 1.0
C6 B:Y8N203 3.6 29.9 1.0
OH B:TYR64 3.6 35.9 1.0
C3 B:Y8N203 3.7 31.1 1.0
C33 B:Y8N203 3.7 29.3 1.0
CB B:GLN99 3.8 31.5 1.0
C34 B:Y8N203 3.8 31.6 1.0
CE1 B:HIS95 3.9 33.8 1.0
CD1 B:TYR96 3.9 30.3 1.0
C1 B:Y8N203 4.1 33.7 1.0
CE1 B:TYR96 4.1 32.7 1.0
C5 B:Y8N203 4.1 29.6 1.0
N7 B:Y8N203 4.2 31.2 1.0
C15 B:Y8N203 4.3 29.8 1.0
C13 B:Y8N203 4.3 27.3 1.0
CE1 B:TYR64 4.4 33.9 1.0
CZ B:TYR64 4.5 34.5 1.0
CA B:TYR96 4.6 30.6 1.0
CD B:GLN99 4.6 33.1 1.0
CG B:TYR96 4.6 30.5 1.0
CG B:HIS95 4.7 33.5 1.0
C14 B:Y8N203 4.7 27.3 1.0
ND1 B:HIS95 4.8 34.0 1.0
C2 B:Y8N203 4.8 28.9 1.0
O B:HIS95 4.8 32.0 1.0
O1 B:Y8N203 4.8 32.3 1.0
C35 B:Y8N203 4.9 32.8 1.0
C32 B:Y8N203 4.9 30.1 1.0
N1 B:Y8N203 4.9 31.4 1.0
CZ B:TYR96 5.0 33.3 1.0

Fluorine binding site 8 out of 18 in 8v39

Go back to Fluorine Binding Sites List in 8v39
Fluorine binding site 8 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:34.7
occ:1.00
 F2 B:Y8N203 0.0 34.7 1.0
C22 B:Y8N203 1.4 35.3 1.0
C23 B:Y8N203 2.4 33.8 1.0
C21 B:Y8N203 2.4 32.6 1.0
N5 B:Y8N203 2.9 32.4 1.0
C10 B:Y8N203 3.0 35.0 1.0
C26 B:Y8N203 3.2 36.5 1.0
C24 B:Y8N203 3.3 37.5 1.0
O B:HOH344 3.6 35.8 1.0
C25 B:Y8N203 3.9 35.9 1.0
O B:HOH331 4.0 36.4 1.0
O B:HOH368 4.1 34.5 1.0
C9 B:Y8N203 4.5 31.7 1.0
O1 B:Y8N203 4.8 32.3 1.0
OD1 B:ASP92 4.8 38.5 1.0

Fluorine binding site 9 out of 18 in 8v39

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Fluorine binding site 9 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:28.7
occ:1.00
 F3 B:Y8N203 0.0 28.7 1.0
C14 B:Y8N203 1.3 27.3 1.0
C15 B:Y8N203 2.4 29.8 1.0
C13 B:Y8N203 2.4 27.3 1.0
S1 B:Y8N203 3.1 25.7 1.0
CG2 B:VAL103 3.2 31.4 1.0
O B:GLN99 3.4 31.5 1.0
CA B:ILE100 3.5 30.2 1.0
C B:GLN99 3.5 31.2 1.0
N B:ILE100 3.6 30.5 1.0
CB B:MET72 3.6 30.6 1.0
C12 B:Y8N203 3.6 29.7 1.0
C16 B:Y8N203 3.7 27.8 1.0
CG1 B:ILE100 3.8 29.1 1.0
CG B:MET72 4.1 30.7 1.0
CB B:GLN99 4.2 31.5 1.0
C11 B:Y8N203 4.2 31.2 1.0
CB B:ILE100 4.3 29.6 1.0
CB B:VAL103 4.4 34.2 1.0
CG1 B:VAL103 4.5 32.7 1.0
CA B:GLN99 4.5 31.7 1.0
CE2 B:PHE78 4.5 28.6 1.0
C32 B:Y8N203 4.6 30.1 1.0
C B:ILE100 4.6 30.9 1.0
C33 B:Y8N203 4.7 29.3 1.0
O B:ILE100 4.8 31.1 1.0
CZ B:PHE78 4.8 28.9 1.0
CA B:MET72 4.9 30.8 1.0
SD B:MET72 4.9 35.8 1.0

Fluorine binding site 10 out of 18 in 8v39

Go back to Fluorine Binding Sites List in 8v39
Fluorine binding site 10 out of 18 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:30.7
occ:1.00
 F4 B:Y8N203 0.0 30.7 1.0
C35 B:Y8N203 1.3 32.8 1.0
F6 B:Y8N203 2.1 31.6 1.0
F5 B:Y8N203 2.2 29.0 1.0
C6 B:Y8N203 2.4 29.9 1.0
C7 B:Y8N203 3.0 27.1 1.0
C11 B:Y8N203 3.1 31.2 1.0
CG1 B:VAL9 3.2 28.7 1.0
C12 B:Y8N203 3.2 29.7 1.0
C5 B:Y8N203 3.4 29.6 1.0
CG2 B:THR58 3.6 30.0 1.0
O B:HOH366 3.6 27.4 1.0
OG1 B:THR58 3.7 30.2 1.0
CB B:VAL9 3.7 28.9 1.0
CB B:THR58 3.8 33.5 1.0
SD B:MET72 4.1 35.8 1.0
C16 B:Y8N203 4.1 27.8 1.0
C13 B:Y8N203 4.1 27.3 1.0
CE B:MET72 4.2 30.8 1.0
C8 B:Y8N203 4.3 30.6 1.0
CA B:VAL9 4.6 28.9 1.0
C3 B:Y8N203 4.6 31.1 1.0
NH2 B:ARG68 4.8 32.5 1.0
CE1 B:TYR96 4.8 32.7 1.0
C15 B:Y8N203 4.9 29.8 1.0
C14 B:Y8N203 4.9 27.3 1.0
CD1 B:TYR96 4.9 30.3 1.0
C33 B:Y8N203 4.9 29.3 1.0
CG B:MET72 4.9 30.7 1.0
C4 B:Y8N203 5.0 31.4 1.0
CG2 B:VAL9 5.0 28.6 1.0
O B:HOH338 5.0 29.3 1.0

Reference:

A.E.Maciag, J.P.Stice, B.Wang, A.K.Sharma, A.H.Chan, K.Lin, D.Singh, M.Dyba, Y.Yang, S.Setoodeh, B.P.Smith, J.H.Ju, S.Jeknic, D.Rabara, Z.Zhang, E.K.Larsen, D.Esposito, J.P.Denson, M.Ranieri, M.Meynardie, S.Mehdizadeh, P.A.Alexander, M.Abreu Blanco, D.M.Turner, R.Xu, F.C.Lightstone, K.K.Wong, A.G.Stephen, K.Wang, D.K.Simanshu, K.W.Sinkevicius, D.V.Nissley, E.Wallace, F.Mccormick, P.J.Beltran. Discovery of Bbo-8520, A First-in-Class Direct and Covalent Dual Inhibitor of Gtp-Bound (on) and Gdp-Bound (Off) KRASG12C. Cancer Discov 2024.
ISSN: ESSN 2159-8290
PubMed: 39642212
DOI: 10.1158/2159-8290.CD-24-0840
Page generated: Sat Feb 8 18:17:44 2025

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