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- PDB-6vkd: Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefu... -

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Basic information

Entry
Database: PDB / ID: 6vkd
TitleCrystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein
ComponentsPrefusion RSV F (DS-Cav1)
KeywordsVIRAL PROTEIN / Inhibitor / complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Chem-R0P / Envelope glycoprotein / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcLellan, J.S.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally ...Title: Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus.
Authors: Vendeville, S. / Tahri, A. / Hu, L. / Demin, S. / Cooymans, L. / Vos, A. / Kwanten, L. / Van den Berg, J. / Battles, M.B. / McLellan, J.S. / Koul, A. / Raboisson, P. / Roymans, D. / Jonckers, T.H.M.
History
DepositionJan 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Prefusion RSV F (DS-Cav1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2569
Polymers63,2181
Non-polymers1,0378
Water1,54986
1
F: Prefusion RSV F (DS-Cav1)
hetero molecules

F: Prefusion RSV F (DS-Cav1)
hetero molecules

F: Prefusion RSV F (DS-Cav1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,76727
Polymers189,6553
Non-polymers3,11224
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area17330 Å2
ΔGint-318 kcal/mol
Surface area49000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.610, 168.610, 168.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-782-

HOH

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Components

#1: Protein Prefusion RSV F (DS-Cav1)


Mass: 63218.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus, (gene. exp.) Human immunodeficiency virus 1
Production host: Homo sapiens (human)
References: UniProt: W8RJF9, UniProt: M1E1E4, UniProt: P03420*PLUS
#2: Chemical ChemComp-R0P / 1-cyclopropyl-3-({1-[3-(methylsulfonyl)propyl]-1H-pyrrolo[3,2-c]pyridin-2-yl}methyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one


Mass: 425.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.64M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5→45.063 Å / Num. obs: 28955 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 53.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.038 / Rrim(I) all: 0.172 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.621.42.0826830131880.50.4582.1331.9100
9.01-45.0616.40.041120607360.9990.010.04347.499.3

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EA3

5ea3


Resolution: 2.5→45.063 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.11
RfactorNum. reflection% reflection
Rfree0.2291 1447 5.01 %
Rwork0.1971 --
obs0.1987 28896 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.21 Å2 / Biso mean: 65.1879 Å2 / Biso min: 27.7 Å2
Refinement stepCycle: final / Resolution: 2.5→45.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 61 86 3558
Biso mean--113.91 51.04 -
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5005-2.58980.33771450.29892679
2.5898-2.69350.33781420.28082677
2.6935-2.81610.30361600.27052692
2.8161-2.96450.27861520.25492670
2.9645-3.15020.25321440.22582715
3.1502-3.39340.24941380.22122730
3.3934-3.73470.25661390.1872734
3.7347-4.27480.21931290.17232774
4.2748-5.38430.16251420.15072805
5.3843-45.0630.20341560.18462973
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)
11.0572-0.4265-0.34712.7942.60365.7566-0.06170.2344-0.3623-0.2444-0.02920.13440.3662-0.25170.1420.3225-0.09470.01010.42780.03880.48643.4761-8.79445.5107
21.81141.84011.2286.70046.18746.8849-0.00940.4188-0.5351-1.16180.7035-0.91180.01740.5333-0.62070.7210.06860.02090.43530.01930.577218.093-12.94437.188
35.7789-0.32330.70724.4344-1.19663.90410.19220.515-1.0321-0.6063-0.18090.24351.2572-0.4309-0.0970.905-0.1119-0.03610.5144-0.18250.88560.4571-23.4396-7.3811
41.54970.0841-0.19683.10992.40524.3708-0.0951-0.034-0.35-0.15050.01920.33510.4655-0.25470.14560.2966-0.0184-0.04630.38250.0740.44464.9065-6.142715.421
50.75440.7290.32988.50041.15392.1482-0.1985-0.1681-0.028-0.40750.16640.31320.0578-0.20290.06360.3558-0.0067-0.02310.45110.09580.40217.7513.045326.2406
63.0862-0.99120.4563.2822-0.28421.8312-0.0165-0.40470.21720.3368-0.0397-0.0931-0.2053-0.08520.02810.41620.03130.03880.4217-0.01090.24214.890320.001832.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 98 )F26 - 98
2X-RAY DIFFRACTION2chain 'F' and (resid 99 through 170 )F99 - 170
3X-RAY DIFFRACTION3chain 'F' and (resid 171 through 238 )F171 - 238
4X-RAY DIFFRACTION4chain 'F' and (resid 239 through 332 )F239 - 332
5X-RAY DIFFRACTION5chain 'F' and (resid 333 through 371 )F333 - 371
6X-RAY DIFFRACTION6chain 'F' and (resid 372 through 506 )F372 - 506

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