RTA in complex with N-(furanylmethyl)-7-carbamoyl-pterin

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


7-Substituted pterins provide a new direction for ricin A chain inhibitors.

Pruet, J.M.Jasheway, K.R.Manzano, L.A.Bai, Y.Anslyn, E.V.Robertus, J.D.

(2011) Eur J Med Chem 46: 3608-3615

  • DOI: https://doi.org/10.1016/j.ejmech.2011.05.025
  • Primary Citation of Related Structures:  
    3PX8, 3PX9

  • PubMed Abstract: 

    Ricin is a potent toxin found in castor seeds. The A chain, RTA, enzymaticlly depurinates a specific adenosine in ribosomal RNA, inhibiting protein synthesis. Ricin is a known chemical weapons threat having no effective antidote. This makes the discovery of new inhibitors of great importance. We have previously used 6-substituted pterins, such as pteroic acid, as an inhibitor platform with moderate success. We now report the success of 7-carboxy pterin (7CP) as an RTA inhibitor; its binding has been monitored using both kinetic and temperature shift assays and by X-ray crystallography. We also discuss the synthesis of various derivatives of 7CP, and their binding affinity and inhibitory effects, as part of a program to make effective RTA inhibitors.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PreproricinA [auth X]258Ricinus 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JP3

Download Ideal Coordinates CCD File 
B [auth X]2-amino-N-(furan-2-ylmethyl)-4-oxo-3,4-dihydropteridine-7-carboxamide
C12 H10 N6 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
JP3 PDBBind:  3PX9 IC50: 3.80e+5 (nM) from 1 assay(s)
BindingDB:  3PX9 IC50: 3.80e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.444α = 90
b = 67.328β = 112.52
c = 49.462γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations