Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence.

Liu, J.Kozhaya, L.Torres, V.J.Unutmaz, D.Lu, M.

(2020) J Biol Chem 295: 5944-5959

  • DOI: https://doi.org/10.1074/jbc.RA120.012697
  • Primary Citation of Related Structures:  
    6U2S, 6U33, 6U3F, 6U3T, 6U3Y, 6U49, 6U4P

  • PubMed Abstract: 

    The rapid emergence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) strains poses a major threat to public health. MRSA possesses an arsenal of secreted host-damaging virulence factors that mediate pathogenicity and blunt immune defenses. Panton-Valentine leukocidin (PVL) and α-toxin are exotoxins that create lytic pores in the host cell membrane. They are recognized as being important for the development of invasive MRSA infections and are thus potential targets for antivirulence therapies. Here, we report the high-resolution X-ray crystal structures of both PVL and α-toxin in their soluble, monomeric, and oligomeric membrane-inserted pore states in complex with n -tetradecylphosphocholine (C 14 PC). The structures revealed two evolutionarily conserved phosphatidylcholine-binding mechanisms and their roles in modulating host cell attachment, oligomer assembly, and membrane perforation. Moreover, we demonstrate that the soluble C 14 PC compound protects primary human immune cells in vitro against cytolysis by PVL and α-toxin and hence may serve as the basis for the development of an antivirulence agent for managing MRSA infections.

  • Organizational Affiliation

    Public Health Research Institute, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G
293Staphylococcus aureusMutation(s): 0 
Gene Names: hlyhla
Membrane Entity: Yes 
Find proteins for P09616 (Staphylococcus aureus)
Explore P09616 
Go to UniProtKB:  P09616
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09616
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PQJ (Subject of Investigation/LOI)
Query on PQJ

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
DA [auth F]
EA [auth G]
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth G],
FA [auth G],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
T [auth D],
V [auth E],
W [auth E],
X [auth E],
Y [auth E]
C19 H43 N O4 P
Query on SO4

Download Ideal Coordinates CCD File 
GA [auth G],
N [auth B],
Q [auth C],
U [auth D],
Z [auth E]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.366α = 90
b = 135.044β = 91.53
c = 132.449γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2020-05-13
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description