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- PDB-5czb: HCV NS5B IN COMPLEX WITH LIGAND IDX17119-5 -

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Basic information

Entry
Database: PDB / ID: 5czb
TitleHCV NS5B IN COMPLEX WITH LIGAND IDX17119-5
ComponentsNS5B
KeywordsREPLICATION / HCV POLYMERASE / Idenix / inhibitor / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / molecular adaptor activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
: / 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 / 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 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 / 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. / 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 / 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
Similarity search - Domain/homology
Chem-55W / DI(HYDROXYETHYL)ETHER / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPierra, C. / Dousson, C. / Augustin, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Synthesis of potent and broad genotypically active NS5B HCV non-nucleoside inhibitors binding to the thumb domain allosteric site 2 of the viral polymerase.
Authors: Pierra Rouviere, C. / Amador, A. / Badaroux, E. / Convard, T. / Da Costa, D. / Dukhan, D. / Griffe, L. / Griffon, J.F. / LaColla, M. / Leroy, F. / Liuzzi, M. / Loi, A.G. / McCarville, J. / ...Authors: Pierra Rouviere, C. / Amador, A. / Badaroux, E. / Convard, T. / Da Costa, D. / Dukhan, D. / Griffe, L. / Griffon, J.F. / LaColla, M. / Leroy, F. / Liuzzi, M. / Loi, A.G. / McCarville, J. / Mascia, V. / Milhau, J. / Onidi, L. / Paparin, J.L. / Rahali, R. / Sais, E. / Seifer, M. / Surleraux, D. / Standring, D. / Dousson, C.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS5B
B: NS5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,02231
Polymers125,2332
Non-polymers3,78829
Water15,205844
1
A: NS5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,91319
Polymers62,6171
Non-polymers2,29618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NS5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,10912
Polymers62,6171
Non-polymers1,49211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.356, 108.234, 134.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NS5B /


Mass: 62616.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1b / Production host: Escherichia coli (E. coli) / References: UniProt: O92972

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Non-polymers , 6 types, 873 molecules

#2: Chemical ChemComp-55W / 1-[4-(7-amino-5-methylpyrazolo[1,5-a]pyrimidin-2-yl)phenyl]-3-{[(R)-(2,4-dimethylphenyl)(methoxy)phosphoryl]amino}-1H-pyrazole-4-carboxylic acid


Mass: 531.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26N7O4P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97244 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97244 Å / Relative weight: 1
ReflectionResolution: 1.96→84.39 Å / Num. obs: 108468 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.63
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.615 / % possible all: 95.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.96→84.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.408 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 2045 1.9 %RANDOM
Rwork0.18821 ---
obs0.18906 106423 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å20 Å2
2--0.29 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.96→84.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8668 0 237 844 9749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199039
X-RAY DIFFRACTIONr_bond_other_d0.0050.028476
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.98812286
X-RAY DIFFRACTIONr_angle_other_deg1.002319467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87751121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8422.423355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.898151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1311577
X-RAY DIFFRACTIONr_chiral_restr0.0870.21387
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022033
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0192.364481
X-RAY DIFFRACTIONr_mcbond_other3.022.3594480
X-RAY DIFFRACTIONr_mcangle_it3.9983.9515603
X-RAY DIFFRACTIONr_mcangle_other3.9983.9515604
X-RAY DIFFRACTIONr_scbond_it4.9633.0224558
X-RAY DIFFRACTIONr_scbond_other4.7652.9424506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1634.7026606
X-RAY DIFFRACTIONr_long_range_B_refined8.19511.79310897
X-RAY DIFFRACTIONr_long_range_B_other8.04811.42210555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.961→2.012 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 153 -
Rwork0.285 7705 -
obs--97.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3184-0.09360.19521.6312-0.45810.81790.08-0.041-0.1406-0.01480.00710.11420.1751-0.0617-0.08710.24050.01-0.03190.01190.01670.0659-25.3224.27612.112
20.13480.1328-0.06631.489-0.17351.63220.03-0.0377-0.05360.3066-0.114-0.16820.23880.10940.0840.3058-0.03-0.03750.02160.02520.033125.8987.26927.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 600
2X-RAY DIFFRACTION2B1 - 600

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