4HUP

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

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: 10.1021/jm3016393
  • Primary Citation of Related Structures:  
    4HV3, 4HV7, 4HUO, 4HUP

  • 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 ...

    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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ricin X267Ricinus communisMutation(s): 0 
EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
19M
Query on 19M
Download Ideal Coordinates CCD File 
X
(2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-3-phenyl-propanoic acid
C27 H26 N8 O6
ANWDLDKKFUMOHP-ROUUACIJSA-N		 Ligand Interaction
MLA
Query on MLA
Download Ideal Coordinates CCD File 
X
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
19MIC50 :  15000   nM  PDBBind
19MIC50:  15000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.723α = 90
b = 67.723β = 90
c = 140.592γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Atomic model
  • Version 1.2: 2013-03-06
    Changes: Database references
  • Version 1.3: 2015-04-29
    Changes: Non-polymer description
  • Version 1.4: 2017-11-15
    Changes: Refinement description