3OZG

Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Acyclic Immucillin Phosphonates: Second-Generation Inhibitors of Plasmodium falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase.

Hazleton, K.Z.Ho, M.C.Cassera, M.B.Clinch, K.Crump, D.R.Rosario, I.Merino, E.F.Almo, S.C.Tyler, P.C.Schramm, V.L.

(2012) Chem Biol 19: 721-730

  • DOI: https://doi.org/10.1016/j.chembiol.2012.04.012
  • Primary Citation of Related Structures:  
    3OZF, 3OZG

  • PubMed Abstract: 

    Plasmodium falciparum, the primary cause of deaths from malaria, is a purine auxotroph and relies on hypoxanthine salvage from the host purine pool. Purine starvation as an antimalarial target has been validated by inhibition of purine nucleoside phosphorylase. Hypoxanthine depletion kills Plasmodium falciparum in cell culture and in Aotus monkey infections. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from P. falciparum is required for hypoxanthine salvage by forming inosine 5'-monophosphate, a branchpoint for all purine nucleotide synthesis in the parasite. Here, we present a class of HGXPRT inhibitors, the acyclic immucillin phosphonates (AIPs), and cell permeable AIP prodrugs. The AIPs are simple, potent, selective, and biologically stable inhibitors. The AIP prodrugs block proliferation of cultured parasites by inhibiting the incorporation of hypoxanthine into the parasite nucleotide pool and validates HGXPRT as a target in malaria.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine-xanthine phosphoribosyltransferase
A, B, C, D
250Plasmodium falciparum FCR-3/GambiaMutation(s): 0 
Gene Names: LACZ
EC: 2.4.2 (PDB Primary Data), 2.4.2.22 (UniProt), 2.4.2.8 (UniProt)
UniProt
Find proteins for P20035 (Plasmodium falciparum (isolate FCR-3 / Gambia))
Explore P20035 
Go to UniProtKB:  P20035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20035
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SSI
Query on SSI

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C],
N [auth D]
[(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid
C11 H17 N4 O5 P
YYXVNWBGVIIBOW-QMMMGPOBSA-N
POP
Query on POP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
O [auth D]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
M [auth C],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SSI PDBBind:  3OZG Ki: 0.65 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.095α = 90
b = 110.628β = 90
c = 173.336γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2012-07-11
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description