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Fluorine in PDB 4ju2: Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12

Enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12

All present enzymatic activity of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12:
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 12, PDB code: 4ju2 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.540, 107.740, 135.820, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4ju2:

The structure of Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12 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 12 (pdb code 4ju2). 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 12, PDB code: 4ju2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 1 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:56.5
occ:1.00
 F19 A:1O03002 0.0 56.5 1.0
C27 A:1O03002 1.4 55.9 1.0
F29 A:1O03002 2.2 52.4 1.0
F30 A:1O03002 2.2 57.1 1.0
C26 A:1O03002 2.4 55.5 1.0
C21 A:1O03002 3.2 55.8 1.0
O20 A:1O03002 3.3 52.9 1.0
C15 A:1O03002 3.4 50.8 1.0
CE A:MET423 3.4 56.8 1.0
C25 A:1O03002 3.4 54.8 1.0
C14 A:1O03002 3.6 50.7 1.0
SD A:MET423 3.8 56.6 1.0
CD2 A:LEU419 3.8 41.9 1.0
C34 A:1O03002 3.8 51.5 1.0
C33 A:1O03002 3.9 53.8 1.0
CG A:LEU419 3.9 41.2 1.0
CG1 A:VAL485 4.1 45.3 1.0
CD1 A:LEU419 4.2 41.8 1.0
CD1 A:LEU489 4.4 52.1 1.0
C16 A:1O03002 4.4 50.5 1.0
C22 A:1O03002 4.6 55.5 1.0
C24 A:1O03002 4.7 57.1 1.0
C13 A:1O03002 4.7 51.3 1.0
C38 A:1O03002 4.9 50.8 1.0
CB A:VAL485 4.9 45.4 1.0
N35 A:1O03002 5.0 54.2 1.0

Fluorine binding site 2 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 2 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:58.0
occ:1.00
 F28 A:1O03002 0.0 58.0 1.0
C3 A:1O03002 1.3 56.0 1.0
C4 A:1O03002 2.4 56.2 1.0
C2 A:1O03002 2.4 56.2 1.0
CB A:ARG422 3.2 48.7 1.0
N A:MET423 3.2 47.6 1.0
C A:ARG422 3.5 48.3 1.0
CB A:MET423 3.6 49.3 1.0
CA A:MET423 3.6 48.0 1.0
C5 A:1O03002 3.6 55.3 1.0
O A:LEU419 3.6 47.4 1.0
C1 A:1O03002 3.7 56.2 1.0
CE2 A:TRP528 3.7 59.5 1.0
NE1 A:TRP528 3.7 59.1 1.0
CD2 A:TRP528 3.7 59.7 1.0
CD1 A:TRP528 3.8 59.6 1.0
CG A:TRP528 3.8 60.9 1.0
CA A:ARG422 3.9 47.4 1.0
O A:ARG422 4.0 50.5 1.0
NE A:ARG422 4.0 49.1 1.0
C6 A:1O03002 4.2 54.9 1.0
CZ A:ARG422 4.2 48.6 1.0
CD A:ARG422 4.3 49.9 1.0
CZ2 A:TRP528 4.3 59.4 1.0
CG A:ARG422 4.3 49.3 1.0
CD1 A:LEU419 4.4 41.8 1.0
CE3 A:TRP528 4.4 57.2 1.0
CB A:TRP528 4.6 61.9 1.0
C A:LEU419 4.6 45.8 1.0
NH2 A:ARG422 4.6 47.6 1.0
NH1 A:ARG422 4.6 48.4 1.0
N A:ARG422 4.6 45.9 1.0
F32 A:1O03002 4.7 56.5 1.0
F31 A:1O03002 4.7 57.3 1.0
CA A:LEU419 4.8 44.1 1.0
CG A:MET423 4.8 50.0 1.0
CH2 A:TRP528 4.8 58.4 1.0
CZ3 A:TRP528 4.9 57.3 1.0

Fluorine binding site 3 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 3 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:52.4
occ:1.00
 F29 A:1O03002 0.0 52.4 1.0
C27 A:1O03002 1.4 55.9 1.0
F30 A:1O03002 2.1 57.1 1.0
F19 A:1O03002 2.2 56.5 1.0
C26 A:1O03002 2.4 55.5 1.0
O20 A:1O03002 2.6 52.9 1.0
C21 A:1O03002 2.9 55.8 1.0
CD2 A:LEU419 3.4 41.9 1.0
C14 A:1O03002 3.5 50.7 1.0
O A:ILE482 3.7 53.1 1.0
CG1 A:VAL485 3.7 45.3 1.0
C25 A:1O03002 3.7 54.8 1.0
CG2 A:ILE482 3.8 51.0 1.0
CB A:VAL485 3.8 45.4 1.0
N A:ALA486 4.1 51.5 1.0
C15 A:1O03002 4.1 50.8 1.0
CA A:ILE482 4.2 52.6 1.0
CG A:LEU419 4.3 41.2 1.0
C22 A:1O03002 4.3 55.5 1.0
C13 A:1O03002 4.4 51.3 1.0
C A:ILE482 4.4 52.7 1.0
C33 A:1O03002 4.4 53.8 1.0
CB A:ALA486 4.5 49.4 1.0
CA A:ALA486 4.5 50.5 1.0
CB A:ILE482 4.6 52.2 1.0
C A:VAL485 4.6 49.9 1.0
CG2 A:VAL485 4.8 41.5 1.0
CA A:VAL485 4.8 48.0 1.0
C24 A:1O03002 4.9 57.1 1.0
C34 A:1O03002 5.0 51.5 1.0

Fluorine binding site 4 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 4 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:57.1
occ:1.00
 F30 A:1O03002 0.0 57.1 1.0
C27 A:1O03002 1.4 55.9 1.0
F29 A:1O03002 2.1 52.4 1.0
F19 A:1O03002 2.2 56.5 1.0
C26 A:1O03002 2.5 55.5 1.0
C33 A:1O03002 3.0 53.8 1.0
C25 A:1O03002 3.0 54.8 1.0
CD1 A:LEU489 3.2 52.1 1.0
CG1 A:VAL485 3.3 45.3 1.0
C34 A:1O03002 3.3 51.5 1.0
N35 A:1O03002 3.5 54.2 1.0
N A:ALA486 3.6 51.5 1.0
CA A:ALA486 3.6 50.5 1.0
C21 A:1O03002 3.7 55.8 1.0
C A:VAL485 3.9 49.9 1.0
CB A:VAL485 4.0 45.4 1.0
CB A:ALA486 4.1 49.4 1.0
C38 A:1O03002 4.1 50.8 1.0
O A:VAL485 4.1 50.3 1.0
O20 A:1O03002 4.2 52.9 1.0
CE A:MET423 4.2 56.8 1.0
C36 A:1O03002 4.2 53.5 1.0
CG A:LEU489 4.4 52.0 1.0
C24 A:1O03002 4.4 57.1 1.0
C37 A:1O03002 4.5 51.9 1.0
CA A:VAL485 4.6 48.0 1.0
O A:ILE482 4.7 53.1 1.0
CB A:LEU489 4.8 52.1 1.0
C22 A:1O03002 4.9 55.5 1.0
C A:ALA486 4.9 50.1 1.0

Fluorine binding site 5 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 5 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:57.3
occ:1.00
 F31 A:1O03002 0.0 57.3 1.0
C1 A:1O03002 1.3 56.2 1.0
C2 A:1O03002 2.4 56.2 1.0
C6 A:1O03002 2.4 54.9 1.0
C7 A:1O03002 2.9 51.5 1.0
C9 A:1O03002 3.1 51.3 1.0
O A:LEU474 3.1 45.8 1.0
N10 A:1O03002 3.2 51.9 1.0
C3 A:1O03002 3.7 56.0 1.0
C5 A:1O03002 3.7 55.3 1.0
CA A:HIS475 3.8 44.4 1.0
CE1 A:TYR477 3.9 42.7 1.0
N8 A:1O03002 4.0 52.2 1.0
CB A:HIS475 4.0 44.4 1.0
NH1 A:ARG422 4.1 48.4 1.0
C A:LEU474 4.1 44.6 1.0
C4 A:1O03002 4.2 56.2 1.0
C11 A:1O03002 4.2 51.0 1.0
N A:HIS475 4.5 44.2 1.0
NH2 A:ARG422 4.6 47.6 1.0
CB A:TRP528 4.6 61.9 1.0
CZ A:ARG422 4.6 48.6 1.0
CD1 A:TYR477 4.7 45.1 1.0
F28 A:1O03002 4.7 58.0 1.0
CD1 A:LEU419 4.8 41.8 1.0
F32 A:1O03002 4.8 56.5 1.0
OH A:TYR477 4.8 41.9 1.0
CZ A:TYR477 4.8 43.6 1.0
C17 A:1O03002 4.9 51.6 1.0

Fluorine binding site 6 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 6 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:56.5
occ:1.00
 F32 A:1O03002 0.0 56.5 1.0
C5 A:1O03002 1.3 55.3 1.0
C4 A:1O03002 2.3 56.2 1.0
C6 A:1O03002 2.4 54.9 1.0
C7 A:1O03002 2.9 51.5 1.0
C16 A:1O03002 3.2 50.5 1.0
CD1 A:LEU497 3.4 40.1 1.0
C3 A:1O03002 3.6 56.0 1.0
CE3 A:TRP528 3.6 57.2 1.0
C1 A:1O03002 3.7 56.2 1.0
N10 A:1O03002 3.8 51.9 1.0
CZ3 A:TRP528 3.8 57.3 1.0
C11 A:1O03002 3.9 51.0 1.0
C2 A:1O03002 4.1 56.2 1.0
C15 A:1O03002 4.2 50.8 1.0
SD A:MET423 4.5 56.6 1.0
CD2 A:TRP528 4.6 59.7 1.0
CG A:LEU497 4.6 41.9 1.0
F28 A:1O03002 4.7 58.0 1.0
CD2 A:LEU497 4.7 38.8 1.0
F31 A:1O03002 4.8 57.3 1.0
CD1 A:LEU419 4.8 41.8 1.0
CH2 A:TRP528 4.9 58.4 1.0

Fluorine binding site 7 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 7 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:70.9
occ:1.00
 F19 B:1O0602 0.0 70.9 1.0
C27 B:1O0602 1.4 70.0 1.0
F29 B:1O0602 2.2 67.8 1.0
F30 B:1O0602 2.2 68.9 1.0
C26 B:1O0602 2.4 69.3 1.0
C25 B:1O0602 3.4 69.6 1.0
C21 B:1O0602 3.4 68.9 1.0
CE B:MET423 3.5 85.9 1.0
O20 B:1O0602 3.6 67.2 1.0
C34 B:1O0602 3.6 67.0 1.0
C33 B:1O0602 3.7 69.4 1.0
CD2 B:LEU419 3.7 67.8 1.0
C15 B:1O0602 3.8 63.9 1.0
C14 B:1O0602 3.9 65.0 1.0
CD1 B:LEU489 4.0 77.7 1.0
SD B:MET423 4.0 85.9 1.0
CG1 B:VAL485 4.0 61.9 1.0
CG B:LEU419 4.1 69.8 1.0
CD1 B:LEU419 4.5 68.5 1.0
C24 B:1O0602 4.6 69.9 1.0
C22 B:1O0602 4.7 69.9 1.0
C38 B:1O0602 4.7 67.0 1.0
CB B:VAL485 4.7 63.1 1.0
N35 B:1O0602 4.7 69.5 1.0
C16 B:1O0602 4.9 62.7 1.0

Fluorine binding site 8 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 8 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:79.0
occ:1.00
 F28 B:1O0602 0.0 79.0 1.0
C3 B:1O0602 1.4 78.9 1.0
C4 B:1O0602 2.4 77.8 1.0
C2 B:1O0602 2.4 78.0 1.0
N B:MET423 3.0 81.2 1.0
CB B:ARG422 3.1 83.8 1.0
C B:ARG422 3.4 82.8 1.0
CE2 B:TRP528 3.4 88.6 1.0
CA B:MET423 3.4 80.6 1.0
CB B:MET423 3.5 82.5 1.0
NE1 B:TRP528 3.6 89.4 1.0
CZ2 B:TRP528 3.7 87.7 1.0
C5 B:1O0602 3.7 74.8 1.0
C1 B:1O0602 3.7 76.1 1.0
CD2 B:TRP528 3.8 90.3 1.0
O B:LEU419 3.8 73.9 1.0
CA B:ARG422 3.9 82.8 1.0
NE B:ARG422 4.0 90.8 1.0
O B:ARG422 4.0 84.0 1.0
CD1 B:TRP528 4.1 90.8 1.0
C6 B:1O0602 4.2 73.6 1.0
CH2 B:TRP528 4.2 88.1 1.0
CG B:TRP528 4.2 92.2 1.0
CD1 B:LEU419 4.3 68.5 1.0
CG B:ARG422 4.3 86.6 1.0
CD B:ARG422 4.3 88.6 1.0
CE3 B:TRP528 4.4 89.3 1.0
CZ B:ARG422 4.5 92.6 1.0
CZ3 B:TRP528 4.6 88.5 1.0
CG B:MET423 4.7 84.1 1.0
N B:ARG422 4.7 81.0 1.0
F32 B:1O0602 4.8 72.9 1.0
F31 B:1O0602 4.8 78.2 1.0
NH2 B:ARG422 4.8 94.7 1.0
C B:LEU419 4.8 73.3 1.0
C B:MET423 5.0 79.9 1.0

Fluorine binding site 9 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 9 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:67.8
occ:1.00
 F29 B:1O0602 0.0 67.8 1.0
C27 B:1O0602 1.4 70.0 1.0
F30 B:1O0602 2.2 68.9 1.0
F19 B:1O0602 2.2 70.9 1.0
C26 B:1O0602 2.5 69.3 1.0
O20 B:1O0602 2.5 67.2 1.0
C21 B:1O0602 2.9 68.9 1.0
CD2 B:LEU419 3.2 67.8 1.0
C14 B:1O0602 3.4 65.0 1.0
CG2 B:ILE482 3.6 70.2 1.0
O B:ILE482 3.7 69.8 1.0
C25 B:1O0602 3.8 69.6 1.0
CB B:VAL485 3.9 63.1 1.0
CG1 B:VAL485 3.9 61.9 1.0
C15 B:1O0602 4.1 63.9 1.0
CA B:ILE482 4.2 70.6 1.0
C13 B:1O0602 4.2 63.3 1.0
CG B:LEU419 4.3 69.8 1.0
C22 B:1O0602 4.3 69.9 1.0
N B:ALA486 4.4 65.7 1.0
C B:ILE482 4.4 70.1 1.0
CB B:ILE482 4.5 70.0 1.0
C33 B:1O0602 4.5 69.4 1.0
CB B:ALA486 4.7 65.1 1.0
CG2 B:VAL485 4.7 63.0 1.0
C B:VAL485 4.7 65.7 1.0
CA B:ALA486 4.8 65.2 1.0
CA B:VAL485 4.9 64.1 1.0
C24 B:1O0602 5.0 69.9 1.0

Fluorine binding site 10 out of 12 in 4ju2

Go back to Fluorine Binding Sites List in 4ju2
Fluorine binding site 10 out of 12 in the Crystal Structure of Hcv NS5B Polymerase in Complex with Compound 12


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

b:68.9
occ:1.00
 F30 B:1O0602 0.0 68.9 1.0
C27 B:1O0602 1.4 70.0 1.0
F29 B:1O0602 2.2 67.8 1.0
F19 B:1O0602 2.2 70.9 1.0
C26 B:1O0602 2.5 69.3 1.0
C25 B:1O0602 3.1 69.6 1.0
C33 B:1O0602 3.1 69.4 1.0
CA B:ALA486 3.4 65.2 1.0
CD1 B:LEU489 3.4 77.7 1.0
N B:ALA486 3.4 65.7 1.0
N35 B:1O0602 3.5 69.5 1.0
CG1 B:VAL485 3.5 61.9 1.0
C34 B:1O0602 3.6 67.0 1.0
CB B:ALA486 3.7 65.1 1.0
C B:VAL485 3.7 65.7 1.0
C21 B:1O0602 3.7 68.9 1.0
CB B:VAL485 3.9 63.1 1.0
O B:VAL485 3.9 67.0 1.0
O20 B:1O0602 4.1 67.2 1.0
C36 B:1O0602 4.3 68.5 1.0
O B:ILE482 4.3 69.8 1.0
C38 B:1O0602 4.4 67.0 1.0
C24 B:1O0602 4.5 69.9 1.0
CA B:VAL485 4.5 64.1 1.0
CG B:LEU489 4.5 76.9 1.0
C37 B:1O0602 4.7 67.8 1.0
CE B:MET423 4.8 85.9 1.0
C B:ALA486 4.8 65.5 1.0
CB B:LEU489 4.8 75.6 1.0
C22 B:1O0602 4.9 69.9 1.0
CD2 B:LEU419 5.0 67.8 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 03:00:03 2024

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