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Fluorine in PDB 5pzp: Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075)

Enzymatic activity of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075)

All present enzymatic activity of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075):
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075), PDB code: 5pzp was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.86 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.200, 90.700, 234.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075) (pdb code 5pzp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075), PDB code: 5pzp:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5pzp

Go back to Fluorine Binding Sites List in 5pzp
Fluorine binding site 1 out of 4 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075)


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 the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:33.5
occ:1.00
 F1 A:8XJ602 0.0 33.5 1.0
C35 A:8XJ602 1.3 36.9 1.0
C34 A:8XJ602 2.3 39.6 1.0
C37 A:8XJ602 2.3 43.0 1.0
H47 A:8XJ602 2.6 46.2 0.0
C21 A:8XJ602 2.8 44.5 1.0
SG A:CYS316 3.0 45.6 1.0
C19 A:8XJ602 3.1 47.9 1.0
NH1 A:ARG200 3.1 23.5 1.0
C2 A:8XJ602 3.1 46.1 1.0
C38 A:8XJ602 3.1 45.4 1.0
CZ A:ARG200 3.1 55.4 1.0
C31 A:8XJ602 3.2 50.0 1.0
O30 A:8XJ602 3.3 51.3 1.0
H46 A:8XJ602 3.3 46.2 0.0
NH2 A:ARG200 3.5 45.0 1.0
C36 A:8XJ602 3.6 42.7 1.0
C33 A:8XJ602 3.6 37.5 1.0
NE A:ARG200 3.6 45.4 1.0
C15 A:8XJ602 3.8 41.5 1.0
SG A:CYS366 3.9 43.9 1.0
CB A:CYS316 3.9 42.1 1.0
N29 A:8XJ602 4.0 49.4 1.0
CD A:ARG200 4.0 33.9 1.0
C32 A:8XJ602 4.1 37.7 1.0
H48 A:8XJ602 4.1 46.2 0.0
H43 A:8XJ602 4.1 41.6 0.0
C18 A:8XJ602 4.2 47.7 1.0
H62 A:8XJ602 4.2 49.2 0.0
C39 A:8XJ602 4.4 42.0 1.0
H64 A:8XJ602 4.5 37.5 0.0
CB A:CYS366 4.5 39.9 1.0
O40 A:8XJ602 4.6 43.8 1.0
C16 A:8XJ602 4.8 45.2 1.0
H57 A:8XJ602 4.8 47.7 0.0
H45 A:8XJ602 4.8 46.0 0.0
C17 A:8XJ602 4.9 45.7 1.0
C20 A:8XJ602 5.0 46.0 1.0

Fluorine binding site 2 out of 4 in 5pzp

Go back to Fluorine Binding Sites List in 5pzp
Fluorine binding site 2 out of 4 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075)


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 the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:47.6
occ:1.00
 F22 A:8XJ602 0.0 47.6 1.0
C25 A:8XJ602 1.4 42.2 1.0
C26 A:8XJ602 2.3 37.8 1.0
C24 A:8XJ602 2.3 41.4 1.0
H61 A:8XJ602 2.6 37.7 0.0
H60 A:8XJ602 2.6 41.4 0.0
CB A:ILE363 3.2 36.8 1.0
CG2 A:ILE363 3.3 31.5 1.0
O A:HOH701 3.5 36.6 1.0
O A:ILE363 3.6 47.9 1.0
C27 A:8XJ602 3.6 38.1 1.0
C23 A:8XJ602 3.6 39.1 1.0
O A:LEU360 3.8 37.9 1.0
C A:ILE363 4.0 45.8 1.0
CD1 A:LEU360 4.0 42.2 1.0
C28 A:8XJ602 4.1 38.3 1.0
CA A:ILE363 4.1 37.1 1.0
CD1 A:ILE363 4.2 42.4 1.0
CG2 A:VAL370 4.2 35.9 1.0
CG1 A:ILE363 4.3 37.1 1.0
H41 A:8XJ602 4.5 38.1 0.0
H42 A:8XJ602 4.5 39.0 0.0
N A:ILE363 4.7 38.9 1.0
CG2 A:VAL321 4.7 34.5 1.0
CD2 A:LEU204 4.8 39.4 1.0
CG1 A:VAL321 4.8 33.7 1.0
CD1 A:LEU204 4.8 35.3 1.0
N A:THR364 4.9 41.3 1.0
C A:LEU360 5.0 41.0 1.0

Fluorine binding site 3 out of 4 in 5pzp

Go back to Fluorine Binding Sites List in 5pzp
Fluorine binding site 3 out of 4 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075)


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 the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:51.4
occ:1.00
 F1 B:8XJ602 0.0 51.4 1.0
C35 B:8XJ602 1.3 48.4 1.0
C34 B:8XJ602 2.3 45.4 1.0
C37 B:8XJ602 2.3 48.1 1.0
H47 B:8XJ602 2.5 48.9 0.0
C21 B:8XJ602 2.8 48.8 1.0
C2 B:8XJ602 3.0 49.0 1.0
NH1 B:ARG200 3.0 39.1 1.0
O30 B:8XJ602 3.1 51.9 1.0
C19 B:8XJ602 3.1 50.4 1.0
C31 B:8XJ602 3.1 49.8 1.0
C38 B:8XJ602 3.1 49.7 1.0
H46 B:8XJ602 3.2 48.9 0.0
SG B:CYS316 3.2 57.5 1.0
CZ B:ARG200 3.3 67.5 1.0
C36 B:8XJ602 3.6 47.2 1.0
C33 B:8XJ602 3.6 43.8 1.0
SG B:CYS366 3.6 52.9 1.0
NE B:ARG200 3.7 59.9 1.0
N29 B:8XJ602 3.8 47.9 1.0
C15 B:8XJ602 3.8 50.1 1.0
NH2 B:ARG200 3.9 55.4 1.0
CD B:ARG200 4.0 45.8 1.0
CB B:CYS316 4.0 53.5 1.0
H48 B:8XJ602 4.0 48.9 0.0
C32 B:8XJ602 4.1 46.5 1.0
C18 B:8XJ602 4.2 49.7 1.0
H62 B:8XJ602 4.2 48.1 0.0
H43 B:8XJ602 4.2 50.1 0.0
H45 B:8XJ602 4.3 49.1 0.0
C39 B:8XJ602 4.3 49.8 1.0
CB B:CYS366 4.4 48.8 1.0
H64 B:8XJ602 4.5 43.9 0.0
O40 B:8XJ602 4.6 47.1 1.0
C20 B:8XJ602 4.6 49.0 1.0
H57 B:8XJ602 4.8 49.7 0.0
C16 B:8XJ602 4.8 50.0 1.0
C17 B:8XJ602 4.9 49.4 1.0

Fluorine binding site 4 out of 4 in 5pzp

Go back to Fluorine Binding Sites List in 5pzp
Fluorine binding site 4 out of 4 in the Crystal Structure of the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075)


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 the Hepatitis C Virus NS5B Rna-Dependent Rna Polymerase in Complex with 4-Fluoro-2-(4-Fluorophenyl)-N-Methyl-5-(2- Methyl-5-{[1-(Pyrimidin-2-Yl)Cyclopropyl]Carbamoyl}Phenyl)-1- Benzofuran-3-Carboxamide (Bms-929075) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:59.5
occ:1.00
 F22 B:8XJ602 0.0 59.5 1.0
C25 B:8XJ602 1.4 57.1 1.0
C26 B:8XJ602 2.3 54.7 1.0
C24 B:8XJ602 2.3 56.4 1.0
H61 B:8XJ602 2.6 54.9 0.0
H60 B:8XJ602 2.6 56.6 0.0
CG2 B:ILE363 3.2 47.9 1.0
CB B:ILE363 3.2 48.9 1.0
C27 B:8XJ602 3.6 52.9 1.0
C23 B:8XJ602 3.6 51.2 1.0
O B:ILE363 3.6 54.5 1.0
O B:LEU360 3.8 60.4 1.0
C B:ILE363 4.0 53.5 1.0
CD1 B:LEU360 4.1 54.2 1.0
CD1 B:ILE363 4.1 49.9 1.0
C28 B:8XJ602 4.1 51.0 1.0
CA B:ILE363 4.1 47.5 1.0
CG1 B:ILE363 4.2 48.0 1.0
CG2 B:VAL370 4.3 55.4 1.0
H42 B:8XJ602 4.5 51.2 0.0
H41 B:8XJ602 4.5 52.8 0.0
CG2 B:VAL321 4.6 54.9 1.0
N B:ILE363 4.7 49.2 1.0
CD1 B:LEU204 4.9 60.1 1.0
CG1 B:VAL321 4.9 54.1 1.0
N B:THR364 4.9 49.4 1.0
CD2 B:LEU204 4.9 58.6 1.0
C B:LEU360 5.0 58.5 1.0

Reference:

K.S.Yeung, B.R.Beno, K.Parcella, J.A.Bender, K.A.Grant-Young, A.Nickel, P.Gunaga, P.Anjanappa, R.O.Bora, K.Selvakumar, K.Rigat, Y.K.Wang, M.Liu, J.Lemm, K.Mosure, S.Sheriff, C.Wan, M.Witmer, K.Kish, U.Hanumegowda, X.Zhuo, Y.Z.Shu, D.Parker, R.Haskell, A.Ng, Q.Gao, E.Colston, J.Raybon, D.M.Grasela, K.Santone, M.Gao, N.A.Meanwell, M.Sinz, M.G.Soars, J.O.Knipe, S.B.Roberts, J.F.Kadow. Discovery of A Hepatitis C Virus NS5B Replicase Palm Site Allosteric Inhibitor (Bms-929075) Advanced to Phase 1 Clinical Studies. J. Med. Chem. V. 60 4369 2017.
ISSN: ISSN 1520-4804
PubMed: 28430437
DOI: 10.1021/ACS.JMEDCHEM.7B00328
Page generated: Tue Jul 15 06:04:24 2025

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