5BSK

Human HGPRT in complex with (S)-HPEPG, an acyclic nucleoside phosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates as Inhibitors of Plasmodium falciparum and Human 6-Oxopurine Phosphoribosyltransferases.

Kaiser, M.M.Hockova, D.Wang, T.H.Dracinsky, M.Postova-Slavetinska, L.Prochazkova, E.Edstein, M.D.Chavchich, M.Keough, D.T.Guddat, L.W.Janeba, Z.

(2015) Chemmedchem 10: 1707-1723

  • DOI: 10.1002/cmdc.201500322
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acyclic nucleoside phosphonates (ANPs) are a promising class of antimalarial therapeutic drug leads that exhibit a wide variety of Ki values for Plasmodium falciparum (Pf) and human hypoxanthine-guanine-(xanthine) phosphoribosyltransferases [HG(X)PRT ...

    Acyclic nucleoside phosphonates (ANPs) are a promising class of antimalarial therapeutic drug leads that exhibit a wide variety of Ki values for Plasmodium falciparum (Pf) and human hypoxanthine-guanine-(xanthine) phosphoribosyltransferases [HG(X)PRTs]. A novel series of ANPs, analogues of previously reported 2-(phosphonoethoxy)ethyl (PEE) and (R,S)-3-hydroxy-2-(phosphonomethoxy)propyl (HPMP) derivatives, were designed and synthesized to evaluate their ability to act as inhibitors of these enzymes and to extend our ongoing antimalarial structure-activity relationship studies. In this series, (S)-3-hydroxy-2-(phosphonoethoxy)propyl (HPEP), (S)-2-(phosphonomethoxy)propanoic acid (CPME), or (S)-2-(phosphonoethoxy)propanoic acid (CPEE) are the acyclic moieties. Of this group, (S)-3-hydroxy-2-(phosphonoethoxy)propylguanine (HPEPG) exhibits the highest potency for PfHGXPRT, with a Ki value of 0.1 μM and a Ki value for human HGPRT of 0.6 μM. The crystal structures of HPEPG and HPEPHx (where Hx=hypoxanthine) in complex with human HGPRT were obtained, showing specific interactions with active site residues. Prodrugs for the HPEP and CPEE analogues were synthesized and tested for in vitro antimalarial activity. The lowest IC50 value (22 μM) in a chloroquine-resistant strain was observed for the bis-amidate prodrug of HPEPG.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 16610 Prague 6 (Czech Republic).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypoxanthine-guanine phosphoribosyltransferase
A, B, C, D
218Homo sapiensMutation(s): 3 
Gene Names: HPRT1 (HPRT)
EC: 2.4.2.8
Find proteins for P00492 (Homo sapiens)
Go to Gene View: HPRT1
Go to UniProtKB:  P00492
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4X7
Query on 4X7

Download SDF File 
Download CCD File 
A, B, C, D
(2-{[(2S)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxypropan-2-yl]oxy}ethyl)phosphonic acid
C10 H16 N5 O6 P
CRTHRZMQPBKEQP-LURJTMIESA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.272α = 90.00
b = 93.279β = 90.00
c = 129.881γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2015-10-07
    Type: Database references