5EA3 | pdb_00005ea3

Crystal Structure of Inhibitor JNJ-2408068 in Complex with Prefusion RSV F Glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.229 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Molecular mechanism of respiratory syncytial virus fusion inhibitors.

Battles, M.B.Langedijk, J.P.Furmanova-Hollenstein, P.Chaiwatpongsakorn, S.Costello, H.M.Kwanten, L.Vranckx, L.Vink, P.Jaensch, S.Jonckers, T.H.Koul, A.Arnoult, E.Peeples, M.E.Roymans, D.McLellan, J.S.

(2016) Nat Chem Biol 12: 87-93

  • DOI: https://doi.org/10.1038/nchembio.1982
  • Primary Citation Related Structures: 
    5EA3, 5EA4, 5EA5, 5EA6, 5EA7, 5EA8

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. Here we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.


  • Organizational Affiliation
    • Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.

Macromolecule Content 

  • Total Structure Weight: 64.4 kDa 
  • Atom Count: 3,361 
  • Modeled Residue Count: 419 
  • Deposited Residue Count: 568 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0A [auth F]568Human respiratory syncytial virus A2Mutation(s): 7 
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03420
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5NK

Query on 5NK



Download:Ideal Coordinates CCD File
I [auth F]2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol
C22 H30 N6 O
RDQSNNMSDOHAPG-UHFFFAOYSA-N
NHE

Query on NHE



Download:Ideal Coordinates CCD File
B [auth F]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth F]
D [auth F]
E [auth F]
F
G [auth F]
C [auth F],
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
5NK BindingDB:  5EA3 EC50: 0.16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.229 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.11α = 90
b = 170.11β = 90
c = 170.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Charles H. Hood FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2016-02-03
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary