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Fluorine in PDB 4ju1: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6:
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 6, PDB code: 4ju1 was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.820, 107.760, 135.860, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4ju1:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6 (pdb code 4ju1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6, PDB code: 4ju1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4ju1

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Fluorine binding site 1 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:60.6
occ:1.00
 F19 A:1NZ3002 0.0 60.6 1.0
C27 A:1NZ3002 1.4 58.9 1.0
F29 A:1NZ3002 2.2 58.8 1.0
F30 A:1NZ3002 2.2 59.7 1.0
C26 A:1NZ3002 2.4 58.2 1.0
C21 A:1NZ3002 3.2 56.5 1.0
O20 A:1NZ3002 3.2 51.4 1.0
C15 A:1NZ3002 3.5 48.0 1.0
C25 A:1NZ3002 3.5 57.4 1.0
C14 A:1NZ3002 3.6 47.5 1.0
O34 A:1NZ3002 3.7 52.8 1.0
SD A:MET423 3.8 46.4 1.0
CD2 A:LEU419 3.9 31.2 1.0
CE A:MET423 4.0 43.8 1.0
C33 A:1NZ3002 4.0 54.9 1.0
CG A:LEU419 4.2 33.5 1.0
CD1 A:LEU489 4.3 44.8 1.0
CG1 A:VAL485 4.4 39.1 1.0
CD1 A:LEU419 4.4 35.3 1.0
C22 A:1NZ3002 4.5 57.2 1.0
C16 A:1NZ3002 4.6 46.7 1.0
C24 A:1NZ3002 4.7 59.5 1.0
C13 A:1NZ3002 4.8 45.6 1.0
C37 A:1NZ3002 4.8 51.0 1.0

Fluorine binding site 2 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 2 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:51.2
occ:1.00
 F28 A:1NZ3002 0.0 51.2 1.0
C3 A:1NZ3002 1.3 51.5 1.0
C4 A:1NZ3002 2.4 53.1 1.0
C2 A:1NZ3002 2.4 52.1 1.0
CB A:ARG422 3.0 39.4 1.0
N A:MET423 3.3 38.7 1.0
C A:ARG422 3.5 39.7 1.0
C5 A:1NZ3002 3.6 52.1 1.0
C1 A:1NZ3002 3.7 52.7 1.0
O A:LEU419 3.7 36.8 1.0
CD2 A:TRP528 3.8 42.8 1.0
CA A:MET423 3.8 39.4 1.0
CG A:TRP528 3.8 43.2 1.0
CE2 A:TRP528 3.8 41.3 1.0
CD1 A:TRP528 3.9 41.9 1.0
CB A:MET423 3.9 41.4 1.0
CA A:ARG422 3.9 39.4 1.0
NE1 A:TRP528 3.9 40.6 1.0
NE A:ARG422 3.9 43.7 1.0
O A:ARG422 4.0 40.8 1.0
CZ A:ARG422 4.1 45.3 1.0
C6 A:1NZ3002 4.2 51.1 1.0
CG A:ARG422 4.2 43.2 1.0
CD A:ARG422 4.2 42.7 1.0
CD1 A:LEU419 4.3 35.3 1.0
CE3 A:TRP528 4.3 38.6 1.0
CB A:TRP528 4.4 45.7 1.0
CZ2 A:TRP528 4.5 39.9 1.0
NH1 A:ARG422 4.5 46.5 1.0
NH2 A:ARG422 4.5 44.7 1.0
C A:LEU419 4.6 35.8 1.0
CA A:LEU419 4.6 34.9 1.0
F32 A:1NZ3002 4.7 51.9 1.0
N A:ARG422 4.7 38.7 1.0
F31 A:1NZ3002 4.7 54.9 1.0
CZ3 A:TRP528 4.9 38.9 1.0
CH2 A:TRP528 4.9 38.6 1.0
O A:THR418 5.0 35.8 1.0

Fluorine binding site 3 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 3 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:58.8
occ:1.00
 F29 A:1NZ3002 0.0 58.8 1.0
C27 A:1NZ3002 1.4 58.9 1.0
F30 A:1NZ3002 2.1 59.7 1.0
F19 A:1NZ3002 2.2 60.6 1.0
C26 A:1NZ3002 2.4 58.2 1.0
O20 A:1NZ3002 2.6 51.4 1.0
C21 A:1NZ3002 2.9 56.5 1.0
CD2 A:LEU419 3.5 31.2 1.0
C14 A:1NZ3002 3.6 47.5 1.0
O A:ILE482 3.7 48.1 1.0
C25 A:1NZ3002 3.8 57.4 1.0
CG1 A:VAL485 3.8 39.1 1.0
CB A:VAL485 3.9 40.7 1.0
CG2 A:ILE482 4.1 42.9 1.0
CA A:ILE482 4.2 46.3 1.0
N A:ALA486 4.2 40.7 1.0
C15 A:1NZ3002 4.3 48.0 1.0
C22 A:1NZ3002 4.3 57.2 1.0
C A:ILE482 4.4 47.2 1.0
CG A:LEU419 4.4 33.5 1.0
C33 A:1NZ3002 4.4 54.9 1.0
C13 A:1NZ3002 4.5 45.6 1.0
CB A:ILE482 4.6 45.4 1.0
CB A:ALA486 4.6 38.8 1.0
CA A:ALA486 4.7 40.8 1.0
CG1 A:ILE482 4.7 43.8 1.0
O34 A:1NZ3002 4.7 52.8 1.0
CG2 A:VAL485 4.8 40.8 1.0
C A:VAL485 4.8 41.2 1.0
C24 A:1NZ3002 4.9 59.5 1.0
CA A:VAL485 4.9 40.7 1.0
CD1 A:LEU489 5.0 44.8 1.0

Fluorine binding site 4 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 4 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:59.7
occ:1.00
 F30 A:1NZ3002 0.0 59.7 1.0
C27 A:1NZ3002 1.4 58.9 1.0
F29 A:1NZ3002 2.1 58.8 1.0
F19 A:1NZ3002 2.2 60.6 1.0
C26 A:1NZ3002 2.5 58.2 1.0
C33 A:1NZ3002 2.9 54.9 1.0
O34 A:1NZ3002 3.0 52.8 1.0
C25 A:1NZ3002 3.0 57.4 1.0
CD1 A:LEU489 3.3 44.8 1.0
CA A:ALA486 3.6 40.8 1.0
CG1 A:VAL485 3.6 39.1 1.0
N A:ALA486 3.6 40.7 1.0
N35 A:1NZ3002 3.7 53.3 1.0
C37 A:1NZ3002 3.7 51.0 1.0
C21 A:1NZ3002 3.8 56.5 1.0
CB A:ALA486 3.9 38.8 1.0
C36 A:1NZ3002 4.1 51.8 1.0
C A:VAL485 4.1 41.2 1.0
CB A:VAL485 4.2 40.7 1.0
O20 A:1NZ3002 4.2 51.4 1.0
CG A:LEU489 4.4 44.7 1.0
C24 A:1NZ3002 4.4 59.5 1.0
O A:VAL485 4.5 41.0 1.0
O A:ILE482 4.6 48.1 1.0
C38 A:1NZ3002 4.6 49.0 1.0
CE A:MET423 4.7 43.8 1.0
CA A:VAL485 4.8 40.7 1.0
CB A:LEU489 4.9 44.5 1.0
C A:ALA486 4.9 41.8 1.0
C22 A:1NZ3002 5.0 57.2 1.0

Fluorine binding site 5 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 5 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:54.9
occ:1.00
 F31 A:1NZ3002 0.0 54.9 1.0
C1 A:1NZ3002 1.3 52.7 1.0
C2 A:1NZ3002 2.4 52.1 1.0
C6 A:1NZ3002 2.4 51.1 1.0
C7 A:1NZ3002 2.9 47.8 1.0
O A:LEU474 3.1 44.4 1.0
C9 A:1NZ3002 3.1 45.6 1.0
N10 A:1NZ3002 3.3 46.8 1.0
C3 A:1NZ3002 3.6 51.5 1.0
C5 A:1NZ3002 3.7 52.1 1.0
CA A:HIS475 3.9 44.2 1.0
N8 A:1NZ3002 4.0 45.0 1.0
CB A:HIS475 4.0 43.2 1.0
CE1 A:TYR477 4.1 41.2 1.0
C A:LEU474 4.1 45.8 1.0
C4 A:1NZ3002 4.2 53.1 1.0
NH1 A:ARG422 4.2 46.5 1.0
NH2 A:ARG422 4.3 44.7 1.0
C11 A:1NZ3002 4.4 46.2 1.0
N A:HIS475 4.5 45.5 1.0
CB A:TRP528 4.5 45.7 1.0
CZ A:ARG422 4.6 45.3 1.0
F28 A:1NZ3002 4.7 51.2 1.0
F32 A:1NZ3002 4.8 51.9 1.0
CD1 A:TYR477 4.9 42.2 1.0
OH A:TYR477 4.9 35.5 1.0
C17 A:1NZ3002 4.9 45.0 1.0
CZ A:TYR477 5.0 39.5 1.0

Fluorine binding site 6 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 6 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3002

b:51.9
occ:1.00
 F32 A:1NZ3002 0.0 51.9 1.0
C5 A:1NZ3002 1.3 52.1 1.0
C4 A:1NZ3002 2.4 53.1 1.0
C6 A:1NZ3002 2.4 51.1 1.0
C7 A:1NZ3002 2.9 47.8 1.0
C16 A:1NZ3002 3.1 46.7 1.0
CD1 A:LEU497 3.5 31.1 1.0
C3 A:1NZ3002 3.6 51.5 1.0
C1 A:1NZ3002 3.7 52.7 1.0
CE3 A:TRP528 3.8 38.6 1.0
N10 A:1NZ3002 3.8 46.8 1.0
C11 A:1NZ3002 3.8 46.2 1.0
CZ3 A:TRP528 3.9 38.9 1.0
C15 A:1NZ3002 4.1 48.0 1.0
C2 A:1NZ3002 4.2 52.1 1.0
CD2 A:LEU497 4.3 32.0 1.0
CG A:LEU497 4.5 32.9 1.0
CD1 A:LEU419 4.6 35.3 1.0
SD A:MET423 4.7 46.4 1.0
F28 A:1NZ3002 4.7 51.2 1.0
CD2 A:TRP528 4.7 42.8 1.0
F31 A:1NZ3002 4.8 54.9 1.0
CH2 A:TRP528 4.9 38.6 1.0

Fluorine binding site 7 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 7 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:66.5
occ:1.00
 F19 B:1NZ602 0.0 66.5 1.0
C27 B:1NZ602 1.4 65.2 1.0
F29 B:1NZ602 2.1 64.2 1.0
F30 B:1NZ602 2.2 66.1 1.0
C26 B:1NZ602 2.5 64.7 1.0
C21 B:1NZ602 3.4 65.3 1.0
O34 B:1NZ602 3.4 58.5 1.0
C25 B:1NZ602 3.4 63.1 1.0
O20 B:1NZ602 3.5 65.5 1.0
SD B:MET423 3.7 71.6 1.0
C33 B:1NZ602 3.7 60.3 1.0
C15 B:1NZ602 3.8 59.1 1.0
C14 B:1NZ602 3.9 61.2 1.0
CE B:MET423 4.0 71.1 1.0
CD1 B:LEU489 4.0 60.3 1.0
CD2 B:LEU419 4.2 59.5 1.0
CG1 B:VAL485 4.2 55.9 1.0
C37 B:1NZ602 4.4 57.4 1.0
CG B:LEU419 4.5 60.2 1.0
CD1 B:LEU419 4.5 59.1 1.0
C22 B:1NZ602 4.7 65.8 1.0
C24 B:1NZ602 4.7 64.5 1.0
N35 B:1NZ602 4.8 57.9 1.0
C16 B:1NZ602 4.9 58.1 1.0
CB B:VAL485 5.0 56.9 1.0

Fluorine binding site 8 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 8 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:71.1
occ:1.00
 F28 B:1NZ602 0.0 71.1 1.0
C3 B:1NZ602 1.3 71.5 1.0
C4 B:1NZ602 2.4 70.7 1.0
C2 B:1NZ602 2.4 71.2 1.0
N B:MET423 2.8 66.7 1.0
CB B:ARG422 3.1 65.6 1.0
CA B:MET423 3.2 67.6 1.0
C B:ARG422 3.3 66.7 1.0
CB B:MET423 3.3 68.7 1.0
CE2 B:TRP528 3.4 81.2 1.0
NE1 B:TRP528 3.5 81.7 1.0
CZ2 B:TRP528 3.6 80.2 1.0
C5 B:1NZ602 3.7 69.2 1.0
O B:LEU419 3.7 61.6 1.0
C1 B:1NZ602 3.7 69.6 1.0
CA B:ARG422 3.8 66.2 1.0
O B:ARG422 3.9 66.6 1.0
CD2 B:TRP528 3.9 82.4 1.0
CD1 B:TRP528 4.0 83.0 1.0
NE B:ARG422 4.1 71.1 1.0
C6 B:1NZ602 4.2 68.0 1.0
CH2 B:TRP528 4.2 80.6 1.0
CG B:TRP528 4.3 84.2 1.0
CG B:ARG422 4.3 67.0 1.0
CD B:ARG422 4.3 69.2 1.0
CG B:MET423 4.5 70.2 1.0
CD1 B:LEU419 4.5 59.1 1.0
CE3 B:TRP528 4.5 80.9 1.0
CZ B:ARG422 4.5 71.4 1.0
N B:ARG422 4.7 65.7 1.0
CZ3 B:TRP528 4.7 80.6 1.0
C B:LEU419 4.7 60.7 1.0
C B:MET423 4.7 67.3 1.0
F32 B:1NZ602 4.7 69.8 1.0
F31 B:1NZ602 4.7 71.2 1.0
NH2 B:ARG422 4.9 70.6 1.0
CA B:LEU419 5.0 59.9 1.0

Fluorine binding site 9 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 9 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:64.2
occ:1.00
 F29 B:1NZ602 0.0 64.2 1.0
C27 B:1NZ602 1.4 65.2 1.0
F19 B:1NZ602 2.1 66.5 1.0
F30 B:1NZ602 2.1 66.1 1.0
C26 B:1NZ602 2.5 64.7 1.0
O20 B:1NZ602 2.5 65.5 1.0
C21 B:1NZ602 2.9 65.3 1.0
CD2 B:LEU419 3.2 59.5 1.0
C14 B:1NZ602 3.4 61.2 1.0
CG2 B:ILE482 3.6 62.0 1.0
C25 B:1NZ602 3.8 63.1 1.0
CG1 B:VAL485 3.8 55.9 1.0
CB B:VAL485 3.9 56.9 1.0
C15 B:1NZ602 4.0 59.1 1.0
CG B:LEU419 4.2 60.2 1.0
O B:ILE482 4.2 63.9 1.0
C13 B:1NZ602 4.2 59.1 1.0
CA B:ILE482 4.3 64.6 1.0
C22 B:1NZ602 4.3 65.8 1.0
CB B:ILE482 4.4 64.0 1.0
C33 B:1NZ602 4.5 60.3 1.0
N B:ALA486 4.5 57.0 1.0
CG2 B:VAL485 4.7 58.0 1.0
CD1 B:LEU419 4.7 59.1 1.0
C B:ILE482 4.7 64.7 1.0
CG1 B:ILE482 4.7 63.5 1.0
O34 B:1NZ602 4.8 58.5 1.0
C24 B:1NZ602 5.0 64.5 1.0

Fluorine binding site 10 out of 12 in 4ju1

Go back to Fluorine Binding Sites List in 4ju1
Fluorine binding site 10 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:66.1
occ:1.00
 F30 B:1NZ602 0.0 66.1 1.0
C27 B:1NZ602 1.4 65.2 1.0
F29 B:1NZ602 2.1 64.2 1.0
F19 B:1NZ602 2.2 66.5 1.0
C26 B:1NZ602 2.5 64.7 1.0
C33 B:1NZ602 3.0 60.3 1.0
C25 B:1NZ602 3.1 63.1 1.0
O34 B:1NZ602 3.3 58.5 1.0
N B:ALA486 3.4 57.0 1.0
CA B:ALA486 3.4 56.6 1.0
CD1 B:LEU489 3.5 60.3 1.0
CG1 B:VAL485 3.6 55.9 1.0
N35 B:1NZ602 3.6 57.9 1.0
C21 B:1NZ602 3.7 65.3 1.0
CB B:ALA486 3.7 54.7 1.0
C B:VAL485 3.9 56.9 1.0
C37 B:1NZ602 3.9 57.4 1.0
CB B:VAL485 3.9 56.9 1.0
C36 B:1NZ602 4.1 56.9 1.0
O20 B:1NZ602 4.1 65.5 1.0
O B:VAL485 4.3 57.2 1.0
O B:ILE482 4.3 63.9 1.0
C24 B:1NZ602 4.5 64.5 1.0
CA B:VAL485 4.6 56.5 1.0
CG B:LEU489 4.7 60.2 1.0
CG2 B:ILE482 4.8 62.0 1.0
C B:ALA486 4.9 56.8 1.0
C38 B:1NZ602 4.9 56.9 1.0
CB B:LEU489 4.9 60.1 1.0
C22 B:1NZ602 4.9 65.8 1.0

Reference:

O.Hucke, R.Coulombe, P.Bonneau, M.Bertrand-Laperle, C.Brochu, J.Gillard, M.A.Joly, S.Landry, O.Lepage, M.Llinas-Brunet, M.Pesant, M.Poirier, M.Poirier, G.Mckercher, M.Marquis, G.Kukolj, P.L.Beaulieu, T.A.Stammers. Molecular Dynamics Simulations and Structure-Based Rational Design Lead to Allosteric Hcv NS5B Polymerase Thumb Pocket 2 Inhibitor with Picomolar Cellular Replicon Potency. J.Med.Chem. V. 57 1932 2014.
ISSN: ISSN 0022-2623
PubMed: 23773186
DOI: 10.1021/JM4004522
Page generated: Thu Aug 1 02:59:41 2024

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