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Fluorine in PDB 4u01: Hcv NS3/4A Serine Protease in Complex with 6570

Protein crystallography data

The structure of Hcv NS3/4A Serine Protease in Complex with 6570, PDB code: 4u01 was solved by C.C.Parsy, F.-R.Alexandre, G.Brandt, C.Caillet, D.Chaves, M.Derock, D.Gloux, Y.Griffon, L.B.Lallos, F.Leroy, M.Liuzzi, A.-G.Loi, B.Mayes, L.Moulat, A.Moussa, M.Chiara, V.Roques, E.Rosinovsky, M.Seifer, A.Stewart, J.Wang, D.Standring, D.Surleraux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.23 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 150.034, 174.363, 133.010, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 29

Other elements in 4u01:

The structure of Hcv NS3/4A Serine Protease in Complex with 6570 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 9 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hcv NS3/4A Serine Protease in Complex with 6570 (pdb code 4u01). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Hcv NS3/4A Serine Protease in Complex with 6570, PDB code: 4u01:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 1 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:47.2
occ:1.00
F13 A:39W301 0.0 47.2 1.0
C1 A:39W301 1.3 49.0 1.0
C2 A:39W301 2.4 49.8 1.0
C3 A:39W301 2.4 49.1 1.0
N7 A:39W301 2.8 48.3 1.0
O11 A:39W301 2.8 51.9 1.0
C12 A:39W301 3.0 58.7 1.0
O A:ASP79 3.4 68.0 1.0
C24 D:39W301 3.6 54.1 1.0
C5 A:39W301 3.6 48.2 1.0
C4 A:39W301 3.6 49.3 1.0
O14 D:39W301 3.6 47.1 1.0
C23 D:39W301 3.7 51.6 1.0
C10 D:39W301 3.7 47.6 1.0
CB A:ASP81 3.8 53.6 1.0
N A:ASP81 3.9 55.5 1.0
C9 D:39W301 3.9 48.0 1.0
O A:VAL78 4.0 59.2 1.0
C A:ASP79 4.1 64.6 1.0
C6 A:39W301 4.1 48.3 1.0
C8 A:39W301 4.1 48.0 1.0
C A:GLN80 4.2 56.9 1.0
C4 D:39W301 4.3 48.1 1.0
CA A:ASP81 4.4 52.7 1.0
CA A:GLN80 4.4 60.0 1.0
N A:GLN80 4.5 60.9 1.0
C8 D:39W301 4.6 48.0 1.0
C10 A:39W301 4.8 48.9 1.0
O A:GLN80 4.8 56.4 1.0
CG A:ASP81 4.8 52.1 1.0
C6 D:39W301 4.8 48.5 1.0
C25 D:39W301 4.9 57.2 1.0
C9 A:39W301 5.0 48.1 1.0
CD A:ARG155 5.0 54.1 1.0
S17 A:39W301 5.0 52.5 1.0

Fluorine binding site 2 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 2 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:57.0
occ:1.00
F13 B:39W301 0.0 57.0 1.0
C1 B:39W301 1.3 57.0 1.0
C2 B:39W301 2.4 56.8 1.0
C3 B:39W301 2.4 57.0 1.0
N7 B:39W301 2.7 56.7 1.0
O11 B:39W301 2.9 57.9 1.0
C12 B:39W301 2.9 61.9 1.0
O14 F:39W301 3.4 55.3 1.0
O B:ASP79 3.5 95.8 1.0
C24 F:39W301 3.6 60.6 1.0
C4 B:39W301 3.6 57.2 1.0
C5 B:39W301 3.6 56.9 1.0
C23 F:39W301 3.7 58.2 1.0
C10 F:39W301 3.7 55.5 1.0
CB B:ASP81 3.9 72.6 1.0
N B:ASP81 4.0 78.0 1.0
O B:VAL78 4.0 84.8 1.0
C9 F:39W301 4.0 56.1 1.0
C8 B:39W301 4.1 56.9 1.0
C6 B:39W301 4.1 56.8 1.0
C B:GLN80 4.1 81.9 1.0
C B:ASP79 4.1 93.5 1.0
CA B:ASP81 4.4 73.5 1.0
C4 F:39W301 4.4 56.2 1.0
CA B:GLN80 4.5 87.9 1.0
N B:GLN80 4.6 89.8 1.0
O B:GLN80 4.6 81.0 1.0
C10 B:39W301 4.8 57.0 1.0
CG B:ASP81 4.8 67.8 1.0
C6 F:39W301 4.8 55.7 1.0
C8 F:39W301 4.9 56.2 1.0
C9 B:39W301 5.0 56.6 1.0
C25 F:39W301 5.0 60.9 1.0
S17 B:39W301 5.0 65.2 1.0

Fluorine binding site 3 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 3 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:59.1
occ:1.00
F13 C:39W301 0.0 59.1 1.0
C1 C:39W301 1.3 60.8 1.0
C2 C:39W301 2.3 60.7 1.0
C3 C:39W301 2.4 61.6 1.0
N7 C:39W301 2.7 61.3 1.0
C12 C:39W301 2.8 62.9 1.0
O11 C:39W301 2.8 61.7 1.0
C4 C:39W301 3.6 60.1 1.0
O C:ASP79 3.6 84.6 1.0
C5 C:39W301 3.6 60.1 1.0
O14 E:39W301 3.7 63.1 1.0
N C:ASP81 3.7 71.1 1.0
C24 E:39W301 3.8 63.0 1.0
CB C:ASP81 3.8 66.4 1.0
C10 E:39W301 3.9 64.2 1.0
C C:GLN80 4.0 73.4 1.0
C23 E:39W301 4.0 62.8 1.0
O C:VAL78 4.1 75.3 1.0
C9 E:39W301 4.1 64.4 1.0
C8 C:39W301 4.1 60.7 1.0
C6 C:39W301 4.1 59.1 1.0
C C:ASP79 4.1 82.2 1.0
CA C:ASP81 4.3 66.9 1.0
CA C:GLN80 4.3 77.5 1.0
N C:GLN80 4.4 79.2 1.0
O C:GLN80 4.6 73.1 1.0
C4 E:39W301 4.6 63.5 1.0
C10 C:39W301 4.7 61.0 1.0
CG C:ASP81 4.9 65.0 1.0
C8 E:39W301 4.9 64.0 1.0
C9 C:39W301 4.9 60.7 1.0
CD C:ARG155 5.0 68.4 1.0
C15 C:39W301 5.0 60.8 1.0

Fluorine binding site 4 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 4 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:49.1
occ:1.00
F13 D:39W301 0.0 49.1 1.0
C1 D:39W301 1.3 48.3 1.0
C2 D:39W301 2.3 47.3 1.0
C3 D:39W301 2.4 49.4 1.0
N7 D:39W301 2.7 47.6 1.0
O11 D:39W301 2.9 49.0 1.0
C12 D:39W301 3.0 52.0 1.0
O14 A:39W301 3.5 49.8 1.0
C4 D:39W301 3.6 48.1 1.0
C10 A:39W301 3.6 48.9 1.0
C5 D:39W301 3.6 48.6 1.0
C24 A:39W301 3.7 56.6 1.0
C23 A:39W301 3.7 55.2 1.0
CB D:ASP81 3.8 49.2 1.0
C9 A:39W301 3.8 48.1 1.0
O D:VAL78 3.9 62.8 1.0
N D:ASP81 3.9 52.5 1.0
C8 D:39W301 4.0 48.0 1.0
O D:ASP79 4.1 67.1 1.0
C6 D:39W301 4.1 48.5 1.0
C D:GLN80 4.1 54.1 1.0
C4 A:39W301 4.2 49.3 1.0
CA D:ASP81 4.3 49.5 1.0
C D:ASP79 4.4 65.0 1.0
CA D:GLN80 4.5 58.3 1.0
C8 A:39W301 4.6 48.0 1.0
N D:GLN80 4.6 60.7 1.0
O D:GLN80 4.6 52.9 1.0
C10 D:39W301 4.7 47.6 1.0
C6 A:39W301 4.7 48.3 1.0
CG D:ASP81 4.7 46.7 1.0
C9 D:39W301 4.9 48.0 1.0
C2 A:39W301 5.0 49.8 1.0
C15 D:39W301 5.0 48.4 1.0
C25 A:39W301 5.0 57.2 1.0

Fluorine binding site 5 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 5 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:62.5
occ:1.00
F13 E:39W301 0.0 62.5 1.0
C1 E:39W301 1.3 63.1 1.0
C2 E:39W301 2.3 62.4 1.0
C3 E:39W301 2.4 64.2 1.0
N7 E:39W301 2.7 63.1 1.0
C12 E:39W301 2.8 67.0 1.0
O11 E:39W301 2.8 65.0 1.0
O14 C:39W301 3.5 60.7 1.0
C5 E:39W301 3.6 63.6 1.0
C4 E:39W301 3.6 63.5 1.0
C24 C:39W301 3.7 61.3 1.0
C10 C:39W301 3.7 61.0 1.0
CB E:ASP81 3.8 75.5 1.0
C9 C:39W301 3.8 60.7 1.0
N E:ASP81 3.8 79.5 1.0
C23 C:39W301 3.8 60.8 1.0
O E:ASP79 4.0 96.7 1.0
C8 E:39W301 4.0 64.0 1.0
C6 E:39W301 4.1 63.2 1.0
O E:VAL78 4.1 85.0 1.0
C E:GLN80 4.1 81.4 1.0
CA E:ASP81 4.3 75.0 1.0
C E:ASP79 4.3 93.4 1.0
CA E:GLN80 4.4 87.1 1.0
N E:GLN80 4.5 88.5 1.0
C4 C:39W301 4.6 60.1 1.0
C8 C:39W301 4.7 60.7 1.0
CG E:ASP81 4.7 73.4 1.0
C10 E:39W301 4.8 64.2 1.0
O E:GLN80 4.8 78.3 1.0
OD2 E:ASP81 4.8 72.2 1.0
CD E:ARG155 4.9 69.7 1.0
C9 E:39W301 4.9 64.4 1.0
C15 E:39W301 4.9 63.4 1.0
S17 E:39W301 4.9 60.6 1.0

Fluorine binding site 6 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 6 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:56.5
occ:1.00
F13 F:39W301 0.0 56.5 1.0
C1 F:39W301 1.3 55.6 1.0
C2 F:39W301 2.3 55.6 1.0
C3 F:39W301 2.4 56.0 1.0
N7 F:39W301 2.7 54.6 1.0
O11 F:39W301 2.8 56.8 1.0
C12 F:39W301 2.8 59.7 1.0
O F:ASP79 3.5 74.2 1.0
CB F:ASP81 3.5 63.6 1.0
C4 F:39W301 3.6 56.2 1.0
C5 F:39W301 3.6 55.9 1.0
N F:ASP81 3.6 67.0 1.0
C24 B:39W301 3.8 64.3 1.0
O14 B:39W301 3.8 57.4 1.0
C9 B:39W301 3.9 56.6 1.0
C F:GLN80 3.9 68.0 1.0
C10 B:39W301 3.9 57.0 1.0
C23 B:39W301 4.0 62.0 1.0
C8 F:39W301 4.1 56.2 1.0
C6 F:39W301 4.1 55.7 1.0
C F:ASP79 4.1 73.8 1.0
CA F:ASP81 4.2 64.8 1.0
O F:VAL78 4.2 71.3 1.0
CA F:GLN80 4.2 70.2 1.0
N F:GLN80 4.4 71.5 1.0
O F:GLN80 4.5 66.9 1.0
C8 B:39W301 4.6 56.9 1.0
CG F:ASP81 4.6 63.1 1.0
C4 B:39W301 4.7 57.2 1.0
C10 F:39W301 4.7 55.5 1.0
CD F:ARG155 4.8 57.6 1.0
C9 F:39W301 4.9 56.1 1.0
S17 F:39W301 4.9 60.0 1.0
C15 F:39W301 4.9 57.0 1.0

Fluorine binding site 7 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 7 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F301

b:57.0
occ:1.00
F13 G:39W301 0.0 57.0 1.0
C1 G:39W301 1.3 58.1 1.0
C2 G:39W301 2.4 57.7 1.0
C3 G:39W301 2.4 58.0 1.0
N7 G:39W301 2.7 57.9 1.0
C12 G:39W301 2.8 62.2 1.0
O11 G:39W301 2.8 58.3 1.0
C5 G:39W301 3.6 58.0 1.0
C4 G:39W301 3.6 57.2 1.0
O G:ASP79 3.6 97.5 1.0
N G:ASP81 3.7 80.6 1.0
CB G:ASP81 3.8 76.8 1.0
C G:GLN80 4.1 82.4 1.0
C6 G:39W301 4.1 57.8 1.0
C8 G:39W301 4.1 58.1 1.0
C G:ASP79 4.1 94.2 1.0
O G:VAL78 4.2 88.9 1.0
CA G:GLN80 4.2 87.0 1.0
CA G:ASP81 4.3 76.1 1.0
N G:GLN80 4.4 89.0 1.0
C10 G:39W301 4.8 57.6 1.0
O G:GLN80 4.8 81.4 1.0
CD G:ARG155 4.9 75.2 1.0
C9 G:39W301 5.0 57.6 1.0
CG G:ASP81 5.0 73.5 1.0

Fluorine binding site 8 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 8 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F301

b:55.8
occ:1.00
F13 H:39W301 0.0 55.8 1.0
C1 H:39W301 1.3 55.5 1.0
C2 H:39W301 2.3 56.3 1.0
C3 H:39W301 2.3 55.6 1.0
N7 H:39W301 2.7 57.0 1.0
C12 H:39W301 2.8 61.0 1.0
O11 H:39W301 2.8 56.4 1.0
O H:ASP79 3.3 89.3 1.0
C5 H:39W301 3.6 56.2 1.0
C4 H:39W301 3.6 55.9 1.0
N H:ASP81 3.9 83.1 1.0
CB H:ASP81 3.9 80.0 1.0
C H:ASP79 4.1 90.3 1.0
C6 H:39W301 4.1 55.5 1.0
C H:GLN80 4.1 82.6 1.0
C8 H:39W301 4.1 57.0 1.0
CA H:GLN80 4.3 85.5 1.0
O H:VAL78 4.4 88.4 1.0
CA H:ASP81 4.4 81.0 1.0
N H:GLN80 4.5 88.1 1.0
O H:GLN80 4.7 80.4 1.0
C10 H:39W301 4.7 55.7 1.0
CD H:ARG155 4.8 79.1 1.0
NE H:ARG155 4.9 80.7 1.0
C9 H:39W301 5.0 56.2 1.0

Fluorine binding site 9 out of 9 in 4u01

Go back to Fluorine Binding Sites List in 4u01
Fluorine binding site 9 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F301

b:77.2
occ:1.00
F13 J:39W301 0.0 77.2 1.0
C1 J:39W301 1.3 76.9 1.0
C3 J:39W301 2.3 77.1 1.0
C2 J:39W301 2.4 77.4 1.0
O11 J:39W301 2.7 76.9 1.0
N7 J:39W301 2.8 76.4 1.0
C12 J:39W301 2.8 75.9 1.0
C5 J:39W301 3.6 77.0 1.0
C4 J:39W301 3.6 77.5 1.0
CB J:ASP81 3.7 0.9 1.0
N J:ASP81 3.7 0.3 1.0
O J:ASP79 4.0 0.3 1.0
O J:VAL78 4.1 0.9 1.0
C6 J:39W301 4.1 76.4 1.0
C J:GLN80 4.1 0.8 1.0
C8 J:39W301 4.2 77.0 1.0
CA J:ASP81 4.3 0.7 1.0
CA J:GLN80 4.3 0.7 1.0
C J:ASP79 4.4 0.4 1.0
N J:GLN80 4.6 0.6 1.0
CG J:ASP81 4.8 96.6 1.0
C10 J:39W301 4.8 76.8 1.0
O J:GLN80 4.8 0.4 1.0
C9 J:39W301 5.0 76.7 1.0

Reference:

C.C.Parsy, F.R.Alexandre, V.Bidau, F.Bonnaterre, G.Brandt, C.Caillet, S.Cappelle, D.Chaves, T.Convard, M.Derock, D.Gloux, Y.Griffon, L.B.Lallos, F.Leroy, M.Liuzzi, A.G.Loi, L.Moulat, M.Chiara, H.Rahali, V.Roques, E.Rosinovsky, S.Savin, M.Seifer, D.Standring, D.Surleraux. Discovery and Structural Diversity of the Hepatitis C Virus NS3/4A Serine Protease Inhibitor Series Leading to Clinical Candidate IDX320. Bioorg.Med.Chem.Lett. V. 25 5427 2015.
ISSN: ESSN 1464-3405
PubMed: 26410074
DOI: 10.1016/J.BMCL.2015.09.009
Page generated: Sun Dec 13 12:12:46 2020

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