Atomistry » Fluorine » PDB 5pzl-5qbz » 5pzp
Atomistry »
  Fluorine »
    PDB 5pzl-5qbz »
      5pzp »

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: Thu Aug 1 12:49:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy