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- PDB-9otw: Influenza A Virus Nucleoprotein(8-498)NP complex with 5-(4-{[(2R)... -

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Basic information

Entry
Database: PDB / ID: 9otw
TitleInfluenza A Virus Nucleoprotein(8-498)NP complex with 5-(4-{[(2R)-6,6-dimethyl-1,4-dioxan-2-yl]methoxy}phenyl)-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide (compound 13)
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: 2.244 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 27, 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

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9595
Polymers113,0822
Non-polymers8773
Water3,027168
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9672
Polymers56,5411
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9923
Polymers56,5411
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.173, 60.173, 582.064
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 phage EcSzw-2 (virus) / References: UniProt: A0A343VTP6
#2: Chemical ChemComp-A1CEF / 5-(4-{[(2R)-6,6-dimethyl-1,4-dioxan-2-yl]methoxy}phenyl)-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide


Mass: 426.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21F3N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
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: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→145.52 Å / Num. obs: 53720 / % possible obs: 100 % / Redundancy: 11.5 % / Rsym value: 0.192 / Net I/σ(I): 8.4
Reflection shellResolution: 2.24→145.52 Å / Num. unique obs: 53720 / CC1/2: 0.543

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
Adxvdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.244→145.52 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.309 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2609 -RANDOM
Rwork0.2445 ---
obs0.2467 52769 98.6 %-
Displacement parametersBiso mean: 69.84 Å2
Baniso -1Baniso -2Baniso -3
1--7.0338 Å20 Å20 Å2
2---7.0338 Å20 Å2
3---14.0675 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.244→145.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6842 0 61 168 7071
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087027HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.879481HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2495SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1242HARMONIC5
X-RAY DIFFRACTIONt_it7027HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion911SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5805SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion17.62
LS refinement shellResolution: 2.244→2.27 Å
RfactorNum. reflection% reflection
Rfree0.4737 53 -
Rwork0.4366 --
obs--67.15 %
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)
10.3670.3108-0.4430.1761-0.68371.1737-0.1064-0.08330.0918-0.08330.07660.04760.09180.04760.02980.51160.0166-0.022-0.18210.0411-0.116710.622429.3249-55.0731
20.07140.0701-0.03981.49280.01281.85610.028-0.18510.3021-0.1851-0.06360.1350.30210.1350.03560.30050.12770.0181-0.09430.0813-0.1396-0.047351.8848-21.9119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A20 - 498
2X-RAY DIFFRACTION1{ A|* }A501
3X-RAY DIFFRACTION2{ B|* }B20 - 499
4X-RAY DIFFRACTION2{ B|* }B501

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