Structure of ricin A chain bound with benzyl-(2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)ethyl)carbamate

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics.

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

(2013) Bioorg Med Chem Lett 23: 6799-6804

  • DOI: https://doi.org/10.1016/j.bmcl.2013.10.017
  • Primary Citation of Related Structures:  
    4MX1, 4MX5

  • PubMed Abstract: 

    Several 7-aminoamido-pterins were synthesized to evaluate the electronic and biochemical subtleties observed in the 'linker space' when N-{N-(pterin-7-yl)carbonylglycyl}-l-phenylalanine 1 was bound to the active site of RTA. The gylcine-phenylalanine dipeptide analogs included both amides and thioamides. Decarboxy gly-phe analog 2 showed a 6.4-fold decrease in potency (IC50 = 128 μM), yet the analogous thioamide 7 recovered the lost activity and performed similarly to the parent inhibitor (IC50 = 29 μM). Thiourea 12 exhibited an IC50 nearly six times lower than the oxo analog 13. All inhibitors showed the pterin head-group firmly bound in their X-ray structures yet the pendants were not fully resolved suggesting that all pendants are not firmly bound in the RTA linker space. Calculated log P values do not correlate to the increase in bioactivity suggesting other factors dominate.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ricin A chainA [auth X]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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5MX

Download Ideal Coordinates CCD File 
B [auth X]benzyl (2-{[(2-amino-4-oxo-3,4-dihydropteridin-7-yl)carbonyl]amino}ethyl)carbamate
C17 H17 N7 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
5MX BindingDB:  4MX5 IC50: 2.80e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.899α = 90
b = 67.899β = 90
c = 140.78γ = 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: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description