Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes.

Li, X.P.Harijan, R.K.Kahn, J.N.Schramm, V.L.Tumer, N.E.

(2020) ACS Infect Dis 6: 1894-1905

  • DOI: https://doi.org/10.1021/acsinfecdis.0c00127
  • Primary Citation of Related Structures:  
    6URW, 6URX, 6URY

  • PubMed Abstract: 

    Ricin toxin A subunit (RTA) removes an adenine from the universally conserved sarcin/ricin loop (SRL) on eukaryotic ribosomes, thereby inhibiting protein synthesis. No high affinity and selective small molecule therapeutic antidotes have been reported against ricin toxicity. RTA binds to the ribosomal P stalk to access the SRL. The interaction anchors RTA to the P protein C-termini at a well-defined hydrophobic pocket, which is on the opposite face relative to the active site. The RTA ribosome binding site has not been previously targeted by small molecule inhibitors. We used fragment screening with surface plasmon resonance to identify small molecular weight lead compounds that bind RTA and defined their interactions by crystallography. We identified five fragments, which bound RTA with mid-micromolar affinity. Three chemically distinct binding fragments were cocrystallized with RTA, and crystal structures were solved. Two fragments bound at the P stalk binding site, and the third bound to helix D, a motif distinct from the P stalk binding site. All fragments bound RTA remote from the catalytic site and caused little change in catalytic site geometry. Two fragments uniquely bound at the hydrophobic pocket with affinity sufficient to inhibit the catalytic activity on eukaryotic ribosomes in the low micromolar range. The binding mode of these inhibitors mimicked the interaction of the P stalk peptide, establishing that small molecule inhibitors can inhibit RTA binding to the ribosome with the potential for therapeutic intervention.

  • Organizational Affiliation

    Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
268Ricinus communisMutation(s): 0 
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02879
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R6T (Subject of Investigation/LOI)
Query on R6T

Download Ideal Coordinates CCD File 
C [auth A]9-oxo-9H-fluorene-4-carboxamide
C14 H9 N O2
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
EA [auth B]
F [auth A]
FA [auth B]
D [auth A],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
IA [auth B]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
R6T Binding MOAD:  6URY IC50: 4.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.228α = 90
b = 66.228β = 90
c = 264.571γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description