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Fluorine in PDB 6bqj: Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)

Protein crystallography data

The structure of Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16), PDB code: 6bqj was solved by H.E.Klei, J.S.Sack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.73 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.440, 57.470, 89.830, 90.00, 115.00, 90.00
R / Rfree (%) 19.7 / 20.6

Other elements in 6bqj:

The structure of Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) (pdb code 6bqj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16), PDB code: 6bqj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6bqj

Go back to Fluorine Binding Sites List in 6bqj
Fluorine binding site 1 out of 6 in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)


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 Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:34.1
occ:1.00
 F A:Z1B301 0.0 34.1 1.0
C7 A:Z1B301 1.4 31.6 1.0
F1 A:Z1B301 2.1 29.3 1.0
C6 A:Z1B301 2.4 30.1 1.0
C5 A:Z1B301 2.9 23.6 1.0
CD1 A:ILE132 3.7 23.8 1.0
O A:Z1B301 3.7 19.8 1.0
N1 A:Z1B301 3.7 20.1 1.0
CA A:LYS136 3.9 24.1 1.0
C4 A:Z1B301 4.0 17.6 1.0
N A:LYS136 4.0 23.3 1.0
C8 A:Z1B301 4.1 32.3 1.0
O6 A:Z1B301 4.1 16.1 1.0
C A:LEU135 4.2 23.5 1.0
O A:LEU135 4.2 19.8 1.0
CG1 A:ILE132 4.2 19.5 1.0
C21 A:Z1B301 4.4 15.7 1.0
O1 A:Z1B301 4.5 32.7 1.0
O A:ILE132 4.5 22.0 1.0
CB A:LEU135 4.6 18.4 1.0
CB A:LYS136 4.6 28.5 1.0
CB A:ALA157 4.7 18.0 1.0
O3 A:Z1B301 4.8 30.7 0.0
C12 A:Z1B301 4.9 17.8 1.0
CA A:LEU135 5.0 19.4 1.0

Fluorine binding site 2 out of 6 in 6bqj

Go back to Fluorine Binding Sites List in 6bqj
Fluorine binding site 2 out of 6 in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)


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 Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:29.3
occ:1.00
 F1 A:Z1B301 0.0 29.3 1.0
C7 A:Z1B301 1.3 31.6 1.0
F A:Z1B301 2.1 34.1 1.0
C6 A:Z1B301 2.4 30.1 1.0
CB A:LEU135 3.3 18.4 1.0
CZ A:PHE154 3.3 19.5 1.0
CB A:ALA157 3.4 18.0 1.0
CE2 A:PHE154 3.7 22.4 1.0
C5 A:Z1B301 3.7 23.6 1.0
O A:LEU135 3.7 19.8 1.0
CD1 A:ILE132 3.8 23.8 1.0
C A:LEU135 3.9 23.5 1.0
N A:ALA157 4.0 17.0 1.0
CD1 A:LEU135 4.2 21.4 1.0
CA A:LEU135 4.2 19.4 1.0
CA A:ALA157 4.3 16.7 1.0
N1 A:Z1B301 4.3 20.1 1.0
O6 A:Z1B301 4.3 16.1 1.0
CG A:LEU135 4.4 22.3 1.0
N A:LYS136 4.4 23.3 1.0
CE1 A:PHE154 4.5 17.8 1.0
C A:ALA156 4.6 18.3 1.0
CA A:LYS136 4.8 24.1 1.0
C8 A:Z1B301 4.9 32.3 1.0
O A:ILE132 4.9 22.0 1.0
C4 A:Z1B301 4.9 17.6 1.0
CG1 A:ILE132 4.9 19.5 1.0
O1 A:Z1B301 5.0 32.7 1.0

Fluorine binding site 3 out of 6 in 6bqj

Go back to Fluorine Binding Sites List in 6bqj
Fluorine binding site 3 out of 6 in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)


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 Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:30.8
occ:1.00
 F B:Z1B301 0.0 30.8 1.0
C7 B:Z1B301 1.4 27.8 1.0
F1 B:Z1B301 2.1 29.6 1.0
C6 B:Z1B301 2.4 24.6 1.0
C5 B:Z1B301 2.9 23.8 1.0
CD1 B:ILE132 3.7 24.7 1.0
N1 B:Z1B301 3.8 20.9 1.0
O B:Z1B301 3.8 18.5 1.0
CA B:LYS136 4.0 25.2 1.0
C4 B:Z1B301 4.1 19.0 1.0
C8 B:Z1B301 4.1 32.5 1.0
N B:LYS136 4.1 24.6 1.0
O6 B:Z1B301 4.1 18.7 1.0
CG1 B:ILE132 4.2 26.1 1.0
O B:LEU135 4.3 20.4 1.0
C B:LEU135 4.3 24.1 1.0
C21 B:Z1B301 4.4 17.7 1.0
O1 B:Z1B301 4.4 34.0 1.0
CB B:LYS136 4.6 29.7 1.0
CB B:LEU135 4.7 20.3 1.0
O B:ILE132 4.7 24.7 1.0
CB B:ALA157 4.8 20.0 1.0
O3 B:Z1B301 4.9 26.8 0.0
C12 B:Z1B301 4.9 18.0 1.0

Fluorine binding site 4 out of 6 in 6bqj

Go back to Fluorine Binding Sites List in 6bqj
Fluorine binding site 4 out of 6 in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)


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 Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:29.6
occ:1.00
 F1 B:Z1B301 0.0 29.6 1.0
C7 B:Z1B301 1.3 27.8 1.0
F B:Z1B301 2.1 30.8 1.0
C6 B:Z1B301 2.4 24.6 1.0
CZ B:PHE154 3.3 19.0 1.0
CB B:LEU135 3.3 20.3 1.0
CB B:ALA157 3.4 20.0 1.0
CE2 B:PHE154 3.7 21.7 1.0
C5 B:Z1B301 3.7 23.8 1.0
O B:LEU135 3.7 20.4 1.0
CD1 B:ILE132 3.8 24.7 1.0
C B:LEU135 3.9 24.1 1.0
N B:ALA157 4.0 18.3 1.0
CA B:LEU135 4.2 20.5 1.0
CD1 B:LEU135 4.2 24.4 1.0
CA B:ALA157 4.3 18.3 1.0
N1 B:Z1B301 4.3 20.9 1.0
O6 B:Z1B301 4.3 18.7 1.0
N B:LYS136 4.3 24.6 1.0
CG B:LEU135 4.4 24.8 1.0
CE1 B:PHE154 4.5 19.0 1.0
C B:ALA156 4.6 19.6 1.0
CA B:LYS136 4.8 25.2 1.0
CG1 B:ILE132 4.8 26.1 1.0
C8 B:Z1B301 4.9 32.5 1.0
O B:ILE132 4.9 24.7 1.0
C4 B:Z1B301 5.0 19.0 1.0
O1 B:Z1B301 5.0 34.0 1.0
C21 B:Z1B301 5.0 17.7 1.0
CA B:ALA156 5.0 17.0 1.0

Fluorine binding site 5 out of 6 in 6bqj

Go back to Fluorine Binding Sites List in 6bqj
Fluorine binding site 5 out of 6 in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)


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 Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:31.9
occ:1.00
 F C:Z1B301 0.0 31.9 1.0
C7 C:Z1B301 1.4 28.3 1.0
F1 C:Z1B301 2.1 29.6 1.0
C6 C:Z1B301 2.4 26.5 1.0
C5 C:Z1B301 3.0 25.0 1.0
CD1 C:ILE132 3.7 26.2 1.0
N1 C:Z1B301 3.8 23.6 1.0
O C:Z1B301 3.8 24.3 1.0
CD C:LYS136 3.9 66.6 1.0
CA C:LYS136 4.0 27.0 1.0
C4 C:Z1B301 4.1 23.6 1.0
CG1 C:ILE132 4.1 23.2 1.0
O6 C:Z1B301 4.1 19.4 1.0
C8 C:Z1B301 4.2 33.1 1.0
N C:LYS136 4.2 26.2 1.0
O C:LEU135 4.2 21.9 1.0
C C:LEU135 4.3 25.5 1.0
C21 C:Z1B301 4.3 21.2 1.0
O1 C:Z1B301 4.5 35.2 1.0
NZ C:LYS136 4.5 96.6 1.0
CB C:LYS136 4.6 31.1 1.0
CG C:LYS136 4.6 50.6 1.0
O C:ILE132 4.7 23.3 1.0
CB C:LEU135 4.7 21.5 1.0
CE C:LYS136 4.8 84.8 1.0
CB C:ALA157 4.8 20.8 1.0
C20 C:Z1B301 4.9 21.4 1.0
C12 C:Z1B301 4.9 20.6 1.0

Fluorine binding site 6 out of 6 in 6bqj

Go back to Fluorine Binding Sites List in 6bqj
Fluorine binding site 6 out of 6 in the Crystal Structure of Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16)


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 Hepatis C Virus Protease (NS3) Complexed with Tripeptidic Acyl Sulfonamide Inhibitor (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:29.6
occ:1.00
 F1 C:Z1B301 0.0 29.6 1.0
C7 C:Z1B301 1.3 28.3 1.0
F C:Z1B301 2.1 31.9 1.0
C6 C:Z1B301 2.4 26.5 1.0
CB C:ALA157 3.4 20.8 1.0
CZ C:PHE154 3.4 19.6 1.0
CB C:LEU135 3.5 21.5 1.0
CD1 C:ILE132 3.7 26.2 1.0
C5 C:Z1B301 3.7 25.0 1.0
O C:LEU135 3.7 21.9 1.0
CE2 C:PHE154 3.7 21.7 1.0
C C:LEU135 3.9 25.5 1.0
N C:ALA157 4.0 19.4 1.0
O6 C:Z1B301 4.2 19.4 1.0
N1 C:Z1B301 4.3 23.6 1.0
CA C:ALA157 4.3 19.4 1.0
CD1 C:LEU135 4.3 26.4 1.0
CA C:LEU135 4.4 21.8 1.0
N C:LYS136 4.4 26.2 1.0
CG C:LEU135 4.5 25.6 1.0
CE1 C:PHE154 4.5 21.3 1.0
C C:ALA156 4.7 19.8 1.0
CG1 C:ILE132 4.7 23.2 1.0
CA C:LYS136 4.8 27.0 1.0
C8 C:Z1B301 4.9 33.1 1.0
O C:ILE132 4.9 23.3 1.0
C21 C:Z1B301 4.9 21.2 1.0
C4 C:Z1B301 4.9 23.6 1.0
O1 C:Z1B301 5.0 35.2 1.0

Reference:

B.Zheng, S.V.D'andrea, L.Q.Sun, A.X.Wang, Y.Chen, P.Hrnciar, J.Friborg, P.Falk, D.Hernandez, F.Yu, A.K.Sheaffer, J.O.Knipe, K.Mosure, R.Rajamani, A.C.Good, K.Kish, J.Tredup, H.E.Klei, M.Paruchuri, A.Ng, Q.Gao, R.A.Rampulla, A.Mathur, N.A.Meanwell, F.Mcphee, P.M.Scola. Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of A Difluoromethyl Group As A Hydrogen-Bond Donor. Acs Med Chem Lett V. 9 143 2018.
ISSN: ISSN 1948-5875
PubMed: 29456803
DOI: 10.1021/ACSMEDCHEMLETT.7B00503
Page generated: Tue Jul 15 10:12:14 2025

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