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- PDB-2qe5: Structure of HCV NS5B Bound to an Anthranilic Acid Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2qe5
TitleStructure of HCV NS5B Bound to an Anthranilic Acid Inhibitor
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / transferase polymerase
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-{[(4-CHLOROPHENOXY)ACETYL]AMINO}BENZOIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChopra, R. / Svenson, K. / Bard, J.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Identification of Anthranilic Acid Derivatives as a Novel Class of Allosteric Inhibitors of Hepatitis C NS5B Polymerase
Authors: Nittoli, T. / Curran, K. / Insaf, S. / DiGrandi, M. / Orlowski, M. / Chopra, R. / Agarwal, A. / Howe, A.Y.M. / Prashad, A. / Floyd, M.B. / Johnson, B. / Sutherland, A. / Wheless, K. / Feld, ...Authors: Nittoli, T. / Curran, K. / Insaf, S. / DiGrandi, M. / Orlowski, M. / Chopra, R. / Agarwal, A. / Howe, A.Y.M. / Prashad, A. / Floyd, M.B. / Johnson, B. / Sutherland, A. / Wheless, K. / Feld, B. / O'Connell, J. / Mansour, T.S. / Bloom, J.
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase
B: RNA-directed RNA polymerase
C: RNA-directed RNA polymerase
D: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,2965
Polymers256,9904
Non-polymers3061
Water1086
1
A: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5532
Polymers64,2481
Non-polymers3061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)64,2481
Polymers64,2481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)64,2481
Polymers64,2481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)64,2481
Polymers64,2481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.340, 101.465, 251.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RNA-directed RNA polymerase / NS5B / p68


Mass: 64247.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1b / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: BK / Gene: NS5B / Production host: Escherichia coli (E. coli) / References: UniProt: Q99AU2, RNA-directed RNA polymerase
#2: Chemical ChemComp-617 / 2-{[(4-CHLOROPHENOXY)ACETYL]AMINO}BENZOIC ACID / 2-(2-(4-CHLOROPHENOXY)ACETAMIDO)BENZOIC ACID


Mass: 305.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12ClNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 26% Polyehtylene Glycol 4000, 50 mM sodium acetate, pH 4.5 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 80230 / Num. obs: 70034 / % possible obs: 87.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.8 Å2 / Rsym value: 0.085 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.28 / % possible all: 79.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1quv

1quv


Resolution: 2.6→19.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2068870.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3559 5.1 %RANDOM
Rwork0.218 ---
obs0.218 69980 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.085 Å2 / ksol: 0.406054 e/Å3
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--7.73 Å20 Å2
3----9.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17368 0 21 6 17395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it17.951.5
X-RAY DIFFRACTIONc_mcangle_it18.312
X-RAY DIFFRACTIONc_scbond_it22.632
X-RAY DIFFRACTIONc_scangle_it22.62.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 562 5 %
Rwork0.274 10704 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2616.parwater.param
X-RAY DIFFRACTION3water.param616.top

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