Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Peptide-conjugated pterins as inhibitors of ricin toxin A.

Saito, R.Pruet, J.M.Manzano, L.A.Jasheway, K.Monzingo, A.F.Wiget, P.A.Kamat, I.Anslyn, E.V.Robertus, J.D.

(2013) J Med Chem 56: 320-329

  • DOI: https://doi.org/10.1021/jm3016393
  • Primary Citation of Related Structures:  
    4HUO, 4HUP, 4HV3, 4HV7

  • PubMed Abstract: 

    Several 7-peptide-substituted pterins were synthesized and tested as competitive active-site inhibitors of ricin toxin A (RTA). Focus began on dipeptide conjugates, and these results further guided the construction of several tripeptide conjugates. The binding of these compounds to RTA was studied via a luminescence-based kinetic assay, as well as through X-ray crystallography. Despite the relatively polar, solvent exposed active site, several hydrophobic interactions, most commonly π-interactions not predicted by modeling programs, were identified in all of the best-performing inhibitors. Nearly all of these compounds provide IC₅₀ values in the low micromolar range.

  • Organizational Affiliation

    Department of Chemistry, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan. anslyn@austin.utexas.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RicinA [auth X]267Ricinus 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 RS8

Download Ideal Coordinates CCD File 
B [auth X]N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine
C18 H17 N7 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
RS8 PDBBind:  4HUO IC50: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.999α = 90
b = 67.999β = 90
c = 140.692γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description