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Fluorine in PDB 4jju: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29:
2.7.7.48; 3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29, PDB code: 4jju was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.070, 108.390, 134.880, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4jju:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29 (pdb code 4jju). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29, PDB code: 4jju:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4jju

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Fluorine binding site 1 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:30.2
occ:1.00
 F19 A:1MB3002 0.0 30.2 1.0
C27 A:1MB3002 1.4 31.5 1.0
F29 A:1MB3002 2.2 32.3 1.0
F30 A:1MB3002 2.2 31.3 1.0
C26 A:1MB3002 2.4 31.4 1.0
O20 A:1MB3002 2.8 26.9 1.0
C21 A:1MB3002 3.0 30.9 1.0
O A:ILE482 3.3 22.8 1.0
CG1 A:VAL485 3.5 21.3 1.0
CB A:VAL485 3.5 23.0 1.0
C25 A:1MB3002 3.6 33.5 1.0
CG2 A:ILE482 3.7 23.7 1.0
CD2 A:LEU419 3.7 21.5 1.0
N A:ALA486 3.7 26.0 1.0
CA A:ILE482 3.9 22.1 1.0
C A:ILE482 4.0 22.1 1.0
C14 A:1MB3002 4.0 25.6 1.0
CA A:ALA486 4.2 27.4 1.0
CB A:ALA486 4.2 25.9 1.0
C A:VAL485 4.3 23.9 1.0
CB A:ILE482 4.3 22.9 1.0
N22 A:1MB3002 4.3 32.4 1.0
CA A:VAL485 4.5 22.6 1.0
CG2 A:VAL485 4.6 22.6 1.0
CG A:LEU419 4.7 22.6 1.0
CG1 A:ILE482 4.7 24.0 1.0
C15 A:1MB3002 4.8 24.5 1.0
C24 A:1MB3002 4.8 35.3 1.0
C13 A:1MB3002 4.9 24.6 1.0

Fluorine binding site 2 out of 10 in 4jju

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Fluorine binding site 2 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:28.8
occ:1.00
 F28 A:1MB3002 0.0 28.8 1.0
C3 A:1MB3002 1.3 25.0 1.0
C2 A:1MB3002 2.4 23.1 1.0
C4 A:1MB3002 2.4 22.9 1.0
N A:MET423 3.1 18.5 1.0
CB A:ARG422 3.1 16.8 1.0
C A:ARG422 3.5 19.1 1.0
CA A:MET423 3.5 17.4 1.0
CB A:MET423 3.6 19.8 1.0
O A:LEU419 3.6 19.9 1.0
C1 A:1MB3002 3.7 23.8 1.0
CD2 A:TRP528 3.7 20.3 1.0
C5 A:1MB3002 3.7 23.8 1.0
CE2 A:TRP528 3.7 19.4 1.0
CG A:TRP528 3.8 20.7 1.0
NE1 A:TRP528 3.8 19.7 1.0
CD1 A:TRP528 3.8 19.3 1.0
CA A:ARG422 3.9 18.1 1.0
O A:ARG422 4.1 19.5 1.0
C6 A:1MB3002 4.2 22.4 1.0
NE A:ARG422 4.2 19.2 1.0
CE3 A:TRP528 4.2 21.3 1.0
CD1 A:LEU419 4.2 22.1 1.0
CD A:ARG422 4.2 18.5 1.0
CG A:ARG422 4.3 18.1 1.0
CZ2 A:TRP528 4.3 22.1 1.0
CZ A:ARG422 4.4 18.9 1.0
CB A:TRP528 4.5 20.1 1.0
C A:LEU419 4.5 19.0 1.0
NH1 A:ARG422 4.6 18.4 1.0
CA A:LEU419 4.7 18.0 1.0
CZ3 A:TRP528 4.7 22.1 1.0
N A:ARG422 4.7 17.2 1.0
CG A:MET423 4.7 20.9 1.0
CH2 A:TRP528 4.7 20.3 1.0
F31 A:1MB3002 4.7 26.6 1.0
NH2 A:ARG422 4.9 18.6 1.0
O A:THR418 5.0 17.8 1.0

Fluorine binding site 3 out of 10 in 4jju

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Fluorine binding site 3 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:32.3
occ:1.00
 F29 A:1MB3002 0.0 32.3 1.0
C27 A:1MB3002 1.4 31.5 1.0
F19 A:1MB3002 2.2 30.2 1.0
F30 A:1MB3002 2.2 31.3 1.0
C26 A:1MB3002 2.4 31.4 1.0
C25 A:1MB3002 2.9 33.5 1.0
CA A:ALA486 3.3 27.4 1.0
CD1 A:LEU489 3.5 29.1 1.0
N A:ALA486 3.5 26.0 1.0
CB A:ALA486 3.6 25.9 1.0
CG1 A:VAL485 3.7 21.3 1.0
C21 A:1MB3002 3.7 30.9 1.0
O A:HOH3188 3.8 28.0 1.0
C A:VAL485 4.0 23.9 1.0
O20 A:1MB3002 4.2 26.9 1.0
CG A:LEU489 4.2 28.4 1.0
C24 A:1MB3002 4.3 35.3 1.0
CB A:VAL485 4.3 23.0 1.0
O A:VAL485 4.4 21.4 1.0
O A:ILE482 4.4 22.8 1.0
C A:ALA486 4.7 27.4 1.0
CA A:VAL485 4.9 22.6 1.0
N22 A:1MB3002 4.9 32.4 1.0
CE A:MET423 5.0 28.5 1.0

Fluorine binding site 4 out of 10 in 4jju

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Fluorine binding site 4 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:31.3
occ:1.00
 F30 A:1MB3002 0.0 31.3 1.0
C27 A:1MB3002 1.4 31.5 1.0
F19 A:1MB3002 2.2 30.2 1.0
F29 A:1MB3002 2.2 32.3 1.0
C26 A:1MB3002 2.4 31.4 1.0
O20 A:1MB3002 2.9 26.9 1.0
C21 A:1MB3002 3.1 30.9 1.0
C25 A:1MB3002 3.5 33.5 1.0
C14 A:1MB3002 3.7 25.6 1.0
C15 A:1MB3002 3.7 24.5 1.0
CD2 A:LEU419 3.9 21.5 1.0
CG1 A:VAL485 3.9 21.3 1.0
CE A:MET423 4.0 28.5 1.0
SD A:MET423 4.1 26.4 1.0
CG A:LEU419 4.4 22.6 1.0
N22 A:1MB3002 4.4 32.4 1.0
O A:HOH3188 4.4 28.0 1.0
CD1 A:LEU489 4.5 29.1 1.0
CB A:VAL485 4.7 23.0 1.0
CD1 A:LEU419 4.7 22.1 1.0
C24 A:1MB3002 4.7 35.3 1.0
CB A:LEU497 4.9 20.2 1.0
C13 A:1MB3002 4.9 24.6 1.0
C16 A:1MB3002 5.0 23.9 1.0

Fluorine binding site 5 out of 10 in 4jju

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Fluorine binding site 5 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:26.6
occ:1.00
 F31 A:1MB3002 0.0 26.6 1.0
C1 A:1MB3002 1.3 23.8 1.0
C2 A:1MB3002 2.4 23.1 1.0
C6 A:1MB3002 2.4 22.4 1.0
C7 A:1MB3002 2.9 23.9 1.0
O A:LEU474 3.0 22.3 1.0
C9 A:1MB3002 3.2 24.6 1.0
N10 A:1MB3002 3.3 24.6 1.0
O A:HOH3196 3.4 23.6 1.0
C3 A:1MB3002 3.6 25.0 1.0
C5 A:1MB3002 3.7 23.8 1.0
CE1 A:TYR477 3.8 21.7 1.0
NH1 A:ARG422 3.9 18.4 1.0
N8 A:1MB3002 3.9 26.6 1.0
CA A:HIS475 3.9 23.7 1.0
C A:LEU474 4.1 21.6 1.0
CB A:HIS475 4.1 24.0 1.0
C4 A:1MB3002 4.2 22.9 1.0
C11 A:1MB3002 4.2 24.4 1.0
N A:HIS475 4.5 22.4 1.0
CB A:TRP528 4.6 20.1 1.0
CZ A:ARG422 4.6 18.9 1.0
CD1 A:TYR477 4.6 21.5 1.0
C17 A:1MB3002 4.7 26.1 1.0
OH A:TYR477 4.7 19.3 1.0
F28 A:1MB3002 4.7 28.8 1.0
NH2 A:ARG422 4.7 18.6 1.0
CZ A:TYR477 4.7 20.7 1.0
C12 A:1MB3002 4.8 24.9 1.0
CD1 A:LEU419 4.9 22.1 1.0

Fluorine binding site 6 out of 10 in 4jju

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Fluorine binding site 6 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:31.6
occ:1.00
 F19 B:1MB602 0.0 31.6 1.0
C27 B:1MB602 1.4 36.5 1.0
F29 B:1MB602 2.2 35.9 1.0
F30 B:1MB602 2.2 35.1 1.0
C26 B:1MB602 2.4 38.1 1.0
O20 B:1MB602 2.7 40.2 1.0
C21 B:1MB602 3.0 40.6 1.0
O B:ILE482 3.2 28.8 1.0
CG2 B:ILE482 3.5 29.2 1.0
CG1 B:VAL485 3.6 24.2 1.0
CB B:VAL485 3.6 24.7 1.0
C25 B:1MB602 3.6 40.6 1.0
CD2 B:LEU419 3.7 26.0 1.0
N B:ALA486 3.7 26.0 1.0
CA B:ILE482 3.9 28.1 1.0
C14 B:1MB602 3.9 37.9 1.0
C B:ILE482 3.9 27.3 1.0
CB B:ALA486 4.2 25.9 1.0
CA B:ALA486 4.2 26.0 1.0
CB B:ILE482 4.2 28.5 1.0
C B:VAL485 4.3 24.7 1.0
N22 B:1MB602 4.3 41.6 1.0
CA B:VAL485 4.5 24.9 1.0
CG2 B:VAL485 4.7 25.9 1.0
C15 B:1MB602 4.7 37.8 1.0
C24 B:1MB602 4.8 42.5 1.0
CG1 B:ILE482 4.8 30.5 1.0
C13 B:1MB602 4.8 36.5 1.0
CG B:LEU419 4.9 28.8 1.0

Fluorine binding site 7 out of 10 in 4jju

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Fluorine binding site 7 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:37.1
occ:1.00
 F28 B:1MB602 0.0 37.1 1.0
C3 B:1MB602 1.3 36.0 1.0
C2 B:1MB602 2.4 35.5 1.0
C4 B:1MB602 2.4 36.1 1.0
N B:MET423 3.0 28.0 1.0
CB B:ARG422 3.2 26.3 1.0
CA B:MET423 3.4 27.7 1.0
C B:ARG422 3.5 28.6 1.0
CB B:MET423 3.5 29.4 1.0
CD2 B:TRP528 3.5 36.9 1.0
CE2 B:TRP528 3.5 36.5 1.0
NE1 B:TRP528 3.6 36.3 1.0
CG B:TRP528 3.6 37.4 1.0
C1 B:1MB602 3.7 35.6 1.0
C5 B:1MB602 3.7 35.0 1.0
CD1 B:TRP528 3.7 37.4 1.0
O B:LEU419 3.9 26.5 1.0
CA B:ARG422 3.9 27.8 1.0
O B:ARG422 4.1 29.5 1.0
CE3 B:TRP528 4.2 36.3 1.0
CZ2 B:TRP528 4.2 35.7 1.0
C6 B:1MB602 4.2 35.4 1.0
NE B:ARG422 4.2 28.7 1.0
CD B:ARG422 4.4 27.3 1.0
CG B:ARG422 4.4 27.1 1.0
CB B:TRP528 4.4 38.9 1.0
CD1 B:LEU419 4.4 28.1 1.0
CZ B:ARG422 4.5 29.6 1.0
CG B:MET423 4.6 32.9 1.0
CH2 B:TRP528 4.7 35.3 1.0
CZ3 B:TRP528 4.7 36.0 1.0
F31 B:1MB602 4.7 35.6 1.0
NH1 B:ARG422 4.7 26.6 1.0
C B:LEU419 4.8 26.2 1.0
N B:ARG422 4.8 26.1 1.0
C B:MET423 4.9 27.1 1.0
CA B:LEU419 5.0 26.4 1.0
NH2 B:ARG422 5.0 30.0 1.0

Fluorine binding site 8 out of 10 in 4jju

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Fluorine binding site 8 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:35.9
occ:1.00
 F29 B:1MB602 0.0 35.9 1.0
C27 B:1MB602 1.4 36.5 1.0
F19 B:1MB602 2.2 31.6 1.0
F30 B:1MB602 2.2 35.1 1.0
C26 B:1MB602 2.4 38.1 1.0
C25 B:1MB602 2.9 40.6 1.0
CA B:ALA486 3.3 26.0 1.0
N B:ALA486 3.4 26.0 1.0
CD1 B:LEU489 3.5 31.4 1.0
CG1 B:VAL485 3.6 24.2 1.0
CB B:ALA486 3.6 25.9 1.0
C21 B:1MB602 3.7 40.6 1.0
C B:VAL485 3.8 24.7 1.0
O B:HOH996 3.9 37.3 1.0
CG B:LEU489 4.1 31.2 1.0
O B:VAL485 4.1 24.7 1.0
O20 B:1MB602 4.2 40.2 1.0
CB B:VAL485 4.2 24.7 1.0
O B:HOH959 4.3 41.3 1.0
C24 B:1MB602 4.3 42.5 1.0
O B:ILE482 4.4 28.8 1.0
C B:ALA486 4.7 26.6 1.0
CA B:VAL485 4.7 24.9 1.0
O B:HOH761 4.7 24.7 1.0
CB B:LEU489 4.9 28.5 1.0
N22 B:1MB602 4.9 41.6 1.0

Fluorine binding site 9 out of 10 in 4jju

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Fluorine binding site 9 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:35.1
occ:1.00
 F30 B:1MB602 0.0 35.1 1.0
C27 B:1MB602 1.4 36.5 1.0
F19 B:1MB602 2.2 31.6 1.0
F29 B:1MB602 2.2 35.9 1.0
C26 B:1MB602 2.4 38.1 1.0
O20 B:1MB602 3.0 40.2 1.0
C21 B:1MB602 3.1 40.6 1.0
C25 B:1MB602 3.5 40.6 1.0
C14 B:1MB602 3.7 37.9 1.0
C15 B:1MB602 3.7 37.8 1.0
CD2 B:LEU419 3.7 26.0 1.0
CG1 B:VAL485 3.8 24.2 1.0
CE B:MET423 4.1 37.2 1.0
O B:HOH959 4.2 41.3 1.0
CD1 B:LEU489 4.3 31.4 1.0
SD B:MET423 4.3 34.5 1.0
CG B:LEU419 4.3 28.8 1.0
N22 B:1MB602 4.4 41.6 1.0
CB B:VAL485 4.6 24.7 1.0
C24 B:1MB602 4.7 42.5 1.0
CD1 B:LEU419 4.7 28.1 1.0
C13 B:1MB602 4.9 36.5 1.0
C16 B:1MB602 4.9 36.7 1.0

Fluorine binding site 10 out of 10 in 4jju

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Fluorine binding site 10 out of 10 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 29


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 Hcv NS5B Polymerase in Complex with Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:35.6
occ:1.00
 F31 B:1MB602 0.0 35.6 1.0
C1 B:1MB602 1.3 35.6 1.0
C2 B:1MB602 2.4 35.5 1.0
C6 B:1MB602 2.4 35.4 1.0
C7 B:1MB602 2.9 34.4 1.0
O B:LEU474 3.0 31.6 1.0
C9 B:1MB602 3.2 35.0 1.0
N10 B:1MB602 3.2 35.4 1.0
O B:HOH870 3.5 34.7 1.0
C3 B:1MB602 3.6 36.0 1.0
C5 B:1MB602 3.7 35.0 1.0
CE1 B:TYR477 3.8 30.9 1.0
NH1 B:ARG422 3.8 26.6 1.0
N8 B:1MB602 4.0 34.2 1.0
CA B:HIS475 4.0 36.6 1.0
C B:LEU474 4.1 33.2 1.0
C4 B:1MB602 4.2 36.1 1.0
CB B:HIS475 4.2 38.2 1.0
C11 B:1MB602 4.2 35.6 1.0
CD1 B:TYR477 4.5 31.1 1.0
N B:HIS475 4.6 34.5 1.0
CZ B:ARG422 4.6 29.6 1.0
OH B:TYR477 4.7 28.9 1.0
CZ B:TYR477 4.7 31.2 1.0
CD1 B:LEU419 4.7 28.1 1.0
F28 B:1MB602 4.7 37.1 1.0
NH2 B:ARG422 4.7 30.0 1.0
C17 B:1MB602 4.8 33.7 1.0
CB B:TRP528 4.8 38.9 1.0
C12 B:1MB602 4.9 34.5 1.0

Reference:

P.L.Beaulieu, R.Coulombe, J.Duan, G.Fazal, C.Godbout, O.Hucke, A.Jakalian, M.A.Joly, O.Lepage, M.Llinas-Brunet, J.Naud, M.Poirier, N.Rioux, B.Thavonekham, G.Kukolj, T.A.Stammers. Structure-Based Design of Novel Hcv NS5B Thumb Pocket 2 Allosteric Inhibitors with Submicromolar GT1 Replicon Potency: Discovery of A Quinazolinone Chemotype. Bioorg.Med.Chem.Lett. V. 23 4132 2013.
ISSN: ISSN 0960-894X
PubMed: 23768906
DOI: 10.1016/J.BMCL.2013.05.037
Page generated: Thu Aug 1 02:51:11 2024

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