4MX1

Structure of ricin A chain bound with 2-amino-4-oxo-N-(2-(3-phenylureido)ethyl)-3,4-dihydropteridine-7-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ricin A chain
A
268Ricinus communisMutation(s): 0 
Find proteins for P02879 (Ricinus communis)
Go to UniProtKB:  P02879
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1MX
Query on 1MX

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Download CCD File 
A
2-amino-4-oxo-N-{2-[(phenylcarbamoyl)amino]ethyl}-3,4-dihydropteridine-7-carboxamide
C16 H16 N8 O3
UGNDSTADFKFZJF-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1MXIC50: 209000 nM (100) BINDINGDB
1MXIC50: 209000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.102α = 90.00
b = 68.102β = 90.00
c = 140.532γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
BOSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references
  • Version 1.2: 2015-04-29
    Type: Non-polymer description
  • Version 1.3: 2017-11-15
    Type: Refinement description