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Fluorine in PDB 5qj1: Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide

Enzymatic activity of Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide

All present enzymatic activity of Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide, PDB code: 5qj1 was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.32 / 2.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.440, 116.550, 64.710, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide (pdb code 5qj1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide, PDB code: 5qj1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5qj1

Go back to Fluorine Binding Sites List in 5qj1
Fluorine binding site 1 out of 2 in the Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide


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 Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:20.0
occ:1.00
 F19 A:J6J601 0.0 20.0 1.0
C16 A:J6J601 1.4 19.6 1.0
C17 A:J6J601 2.3 18.9 1.0
C15 A:J6J601 2.3 18.1 1.0
H50 A:J6J601 2.6 20.3 1.0
H49 A:J6J601 2.6 20.3 1.0
CG2 A:ILE363 3.3 19.1 1.0
CB A:ILE363 3.4 20.4 1.0
O A:HOH713 3.5 16.5 1.0
C18 A:J6J601 3.6 19.3 1.0
C14 A:J6J601 3.6 17.1 1.0
CD1 A:ILE363 4.0 22.0 1.0
O A:ILE363 4.1 20.5 1.0
CD1 A:LEU360 4.1 23.4 1.0
C13 A:J6J601 4.1 18.0 1.0
CG1 A:VAL321 4.2 19.4 1.0
O A:LEU360 4.2 19.2 1.0
CG1 A:ILE363 4.3 19.9 1.0
CD2 A:LEU204 4.3 20.4 1.0
CD1 A:LEU204 4.4 16.9 1.0
CG2 A:VAL321 4.4 19.1 1.0
H51 A:J6J601 4.5 20.3 1.0
H48 A:J6J601 4.5 20.3 1.0
C A:ILE363 4.5 21.3 1.0
CA A:ILE363 4.6 18.4 1.0
CB A:VAL321 4.9 19.6 1.0
CG2 A:VAL370 4.9 17.2 1.0
CG A:LEU204 4.9 18.8 1.0

Fluorine binding site 2 out of 2 in 5qj1

Go back to Fluorine Binding Sites List in 5qj1
Fluorine binding site 2 out of 2 in the Crystal Structure of the Hepatitis C Virus Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide


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 Genotype 2A Strain JFH1 L30S NS5B Rna-Dependent Rna Polymerase in Complex with 6- (Ethylamino)-2-(4-Fluorophenyl)-5-(3-{[1-(5-Fluoropyrimidin-2-Yl) Cyclopropyl]Carbamoyl}-4-Methoxyphenyl)-N-Methyl-1-Benzofuran-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:40.3
occ:1.00
 F42 A:J6J601 0.0 40.3 1.0
C37 A:J6J601 1.4 33.9 1.0
C38 A:J6J601 2.4 30.6 1.0
C36 A:J6J601 2.4 30.2 1.0
H65 A:J6J601 2.7 20.3 1.0
H64 A:J6J601 2.7 20.3 1.0
O A:GLN194 3.5 25.5 1.0
N39 A:J6J601 3.6 34.9 1.0
N35 A:J6J601 3.6 34.8 1.0
C A:GLN194 3.8 25.0 1.0
C A:TYR195 3.9 21.5 1.0
N A:SER196 3.9 17.6 1.0
O A:HOH796 4.0 54.1 1.0
C34 A:J6J601 4.0 33.1 1.0
N A:TYR195 4.2 19.8 1.0
O A:TYR195 4.2 21.6 1.0
CA A:TYR195 4.3 18.3 1.0
CA A:SER196 4.5 17.1 1.0
CA A:GLN194 4.6 19.9 1.0
O A:PHE193 4.6 29.5 1.0
CB A:SER196 4.9 18.2 1.0
OE1 A:GLN199 4.9 21.2 1.0

Reference:

K.S.Yeung, B.R.Beno, K.Mosure, J.Zhu, K.A.Grant-Young, K.Parcella, P.Anjanappa, R.O.Bora, K.Selvakumar, Y.K.Wang, H.Fang, R.Krause, K.Rigat, M.Liu, J.Lemm, S.Sheriff, M.Witmer, J.Tredup, A.Jardel, K.Kish, D.Parker, R.Haskell, K.Santone, N.A.Meanwell, M.G.Soars, S.B.Roberts, J.F.Kadow. Structure-Property Basis For Solving Transporter-Mediated Efflux and Pan-Genotypic Inhibition in Hcv NS5B Inhibitors. Acs Med Chem Lett V. 9 1217 2018.
ISSN: ISSN 1948-5875
PubMed: 30613329
DOI: 10.1021/ACSMEDCHEMLETT.8B00379
Page generated: Thu Aug 1 13:16:01 2024

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