1ULB

APPLICATION OF CRYSTALLOGRAPHIC AND MODELING METHODS IN THE DESIGN OF PURINE NUCLEOSIDE PHOSPHORYLASE INHIBITORS

• PDB DOI: https://doi.org/10.2210/pdb1ULB/pdb

• Classification: PENTOSYLTRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1991-11-05 Released: 1993-01-15 
• Deposition Author(s): Ealick, S.E., Rule, S.A., Carter, D.C., Greenhough, T.J., Babu, Y.S., Cook, W.J., Habash, J., Helliwell, J.R., Stoeckler, J.D., Parksjunior, R.E., Chen, S.-F., Bugg, C.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Observed: 0.204 

Literature

Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors.

Ealick, S.E., Babu, Y.S., Bugg, C.E., Erion, M.D., Guida, W.C., Montgomery, J.A., Secrist 3rd., J.A.

(1991) Proc Natl Acad Sci U S A 88: 11540-11544

• PubMed: 1763067 
• DOI: https://doi.org/10.1073/pnas.88.24.11540
• Primary Citation of Related Structures:  
  1ULA, 1ULB


• PubMed Abstract: 
  

  Competitive inhibitors of the salvage pathway enzyme purine-nucleoside phosphorylase (purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1) have been designed by using the three-dimensional structure of the enzyme as determined by x-ray crystallography. The process was an iterative one that utilized interactive computer graphics, Monte Carlo-based conformational searching, energy minimization, and x-ray crystallography. The proposed compounds were synthesized and tested by an in vitro assay. Among the compounds designed and synthesized are the most potent competitive inhibitors of purine nucleoside phosphorylase thus far reported.

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Organizational Affiliation: 

University of Alabama, Birmingham 35294.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 32.53 kDa 
• Atom Count: 2,279 
• Modelled Residue Count: 289 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PURINE NUCLEOSIDE PHOSPHORYLASE	A	289	Homo sapiens	Mutation(s): 0  EC: 2.4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens) Explore P00491  Go to UniProtKB:  P00491
PHAROS:  P00491 GTEx:  ENSG00000198805

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GUN	D [auth A]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Observed: 0.204 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.9	α = 90
b = 142.9	β = 90
c = 165.2	γ = 120

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-01-15 
Deposition Author(s): Ealick, S.E., Rule, S.A., Carter, D.C., Greenhough, T.J., Babu, Y.S., Cook, W.J., Habash, J., Helliwell, J.R., Stoeckler, J.D., Parksjunior, R.E., Chen, S.-F., Bugg, C.E.

Revision History  

• Version 1.0: 1993-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other