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- PDB-9oug: Influenza A Virus Nucleoprotein(8-498)NP complex with rac-5-(4-((... -

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Basic information

Entry
Database: PDB / ID: 9oug
TitleInfluenza A Virus Nucleoprotein(8-498)NP complex with rac-5-(4-(((2R,6R)-6-(methoxymethyl)-6-methyl-1,4-dioxan-2-yl)methoxy)phenyl)-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide (Compound 20)
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nucleocapsid protein Nucleoprotein
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMamo, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Optimization of a Novel Series of Influenza A Virus Replication Inhibitors Targeting the Nucleoprotein Protein-Protein Interaction.
Authors: Taft, B.R. / Hesse, M.J. / Mamo, M. / Bussiere, D.E. / Huang, R. / Lee, P.S. / Wedel, L. / Growcott, E. / Wolff, K.C. / Kuhen, K. / Abend, J. / Wong, K.A. / Ganem, D. / Leonard, V.H.J. / Tully, D.C.
History
DepositionMay 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9954
Polymers113,0822
Non-polymers9132
Water2,756153
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9972
Polymers56,5411
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9972
Polymers56,5411
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.151, 60.151, 584.428
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 56541.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/(Puerto Rico/8/1934-Korea/426/1968)(H2N2))
Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A343VTP6
#2: Chemical ChemComp-A1CEO / 5-(4-{[(2R,6S)-6-(methoxymethyl)-6-methyl-1,4-dioxan-2-yl]methoxy}phenyl)-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide


Mass: 456.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23F3N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 22.5% PEG800, 0.1 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→46.44 Å / Num. obs: 48313 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.979 / Net I/σ(I): 6.2
Reflection shellResolution: 2.33→2.46 Å / Rmerge(I) obs: 1.694 / Num. unique obs: 6831 / CC1/2: 0.424

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
Adxvdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→46.44 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.855 / SU R Cruickshank DPI: 0.372 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.393 / SU Rfree Blow DPI: 0.288 / SU Rfree Cruickshank DPI: 0.284
RfactorNum. reflection% reflectionSelection details
Rfree0.3216 2389 -RANDOM
Rwork0.272 ---
obs0.2744 48107 99.9 %-
Displacement parametersBiso mean: 54.07 Å2
Baniso -1Baniso -2Baniso -3
1-3.6881 Å20 Å20 Å2
2--3.6881 Å20 Å2
3----7.3762 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.33→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 64 153 6989
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076956HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.869375HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2486SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1225HARMONIC5
X-RAY DIFFRACTIONt_it6956HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion900SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5479SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion16.98
LS refinement shellResolution: 2.33→2.35 Å
RfactorNum. reflection% reflection
Rfree0.3794 43 -
Rwork0.3628 --
obs0.3635 963 98.6 %
Refinement TLS params.

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)
10.53940.3842-0.49020.8072-0.60910.7684-0.0551-0.08360.0677-0.08360.0413-0.01290.0677-0.01290.01380.31070.0031-0.0511-0.12120.0786-0.155510.530229.3-55.1643
20.63840.0288-0.0061.8539-0.11641.5867-0.0527-0.07470.2816-0.0747-0.02630.06220.28160.06220.0790.24420.03750.0015-0.09270.1185-0.15730.13652.369-22.2632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A20 - 499
2X-RAY DIFFRACTION2{ B|* }B20 - 498

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