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

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Basic information

Entry
Database: PDB / ID: 9ouc
TitleInfluenza A Virus Nucleoprotein(8-498)NP complex with 5-(4-(morpholinomethyl)phenyl)-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide (Compound 3)
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nucleocapsid protein Nucleoprotein
Function / homology
Function and homology information


cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / vRNA Synthesis ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / helical viral capsid / Viral mRNA Translation / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding / plasma membrane
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: 2.732 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

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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)113,8695
Polymers113,0822
Non-polymers7873
Water4,071226
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9222
Polymers56,5411
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9473
Polymers56,5411
Non-polymers4062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.968, 96.861, 285.255
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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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: P03466
#2: Chemical ChemComp-A1CEM / 5-{4-[(morpholin-4-yl)methyl]phenyl}-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide


Mass: 381.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18F3N3O3
#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.: 226 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
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: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→142.63 Å / Num. obs: 26838 / % possible obs: 98 % / Redundancy: 13.2 % / CC1/2: 0.96 / Net I/σ(I): 3.8
Reflection shellResolution: 2.73→2.88 Å / Redundancy: 14.6 % / Num. unique obs: 3949 / CC1/2: 0.463 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
Adxvdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.732→142.63 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.801 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.429
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1300 -RANDOM
Rwork0.266 ---
obs0.2681 26417 96.7 %-
Displacement parametersBiso mean: 54.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.8772 Å20 Å20 Å2
2---1.2917 Å20 Å2
3----1.5856 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.732→142.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 55 226 6845
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.99083HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2390SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1187HARMONIC5
X-RAY DIFFRACTIONt_it6736HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5574SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion17.53
LS refinement shellResolution: 2.732→2.75 Å
RfactorNum. reflection% reflection
Rfree0.3441 39 -
Rwork0.3099 --
obs--99.25 %
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)
10.92480.29890.42160.4667-0.22751.7375-0.13360.1099-0.24190.10990.0186-0.0784-0.2419-0.07840.1150.1295-0.0218-0.0605-0.07950.0092-0.193931.30098.576-21.7003
20.50630.09310.47130.7144-0.01080.66430.11990.02820.07260.0282-0.0435-0.17250.0726-0.1725-0.07640.0537-0.1119-0.02810.05310.0264-0.194533.721736.1204-52.1015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A21 - 497
2X-RAY DIFFRACTION2{ B|* }B21 - 497

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