4ESI | pdb_00004esi

Structure of ricin A chain bound with N-((1H-1,2,3-triazol-4-yl)methyl-2-amino-4-oxo-3,4-dihydropteridine-7-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb4ESI/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Ricinus communis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-23 Released: 2012-10-31 
• Deposition Author(s): Jasheway, K.R., Pruet, J.M., Ryoto, S., Manzano, L.A., Wiget, P.A., Kamat, I., Anslyn, E.V., Monzingo, A.F., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.285 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Optimized 5-membered heterocycle-linked pterins for the inhibition of Ricin Toxin A.

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

(2012) ACS Med Chem Lett 3: 588-591

• PubMed: 23050058 
• DOI: https://doi.org/10.1021/ml300099t
• Primary Citation Related Structures: 
  4ESI


• PubMed Abstract: 
  

  The optimization of a series of pterin amides for use as Ricin Toxin A (RTA) inhibitors is reported. Based upon crystallographic data of a previous furan-linked pterin, various expanded furans were synthesized, linked to the pterin and tested for inhibition. Concurrently, hetero-analogs of furan were explored, leading to the discovery of more potent triazol-linked pterins. Additionally, we discuss a dramatic improvement in the synthesis of these pterin amides via a dual role by diazabicycloundecene (DBU). This synthetic enhancement facilitates rapid diversification of the previously challenging pterin heterocycle, potentially aiding future medicinal research involving this structure.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.22 kDa 
• Atom Count: 2,248 
• Modeled Residue Count: 261 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin	A	267	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0RB	B [auth A]	2-amino-4-oxo-N-(1H-1,2,3-triazol-5-ylmethyl)-1,4-dihydropteridine-7-carboxamide C10 H9 N9 O2 IOLZYHQWMHJFBL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.285 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.359	α = 90
b = 68.359	β = 90
c = 141.088	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Jasheway, K.R., Pruet, J.M., Ryoto, S., Manzano, L.A., Wiget, P.A., Kamat, I., Anslyn, E.V., Monzingo, A.F., Robertus, J.D.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description