5W8V

HUMAN HGPRT in complex with [(2-[(guanin-9-yl)methyl]propane-1,3-diyl)bis(oxy)]bis(methylene)diphosphonic acid

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-06-22 Released: 2017-08-30 
  • Deposition Author(s): Guddat, L.W., Keough, D.T.
  • Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Czech Science Foundation, Institute of Organic Chemistry and Biochemistry, Gilead Sciences

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Synthesis and Evaluation of Asymmetric Acyclic Nucleoside Bisphosphonates as Inhibitors of Plasmodium falciparum and Human Hypoxanthine-Guanine-(Xanthine) Phosphoribosyltransferase.

Spacek, P.Keough, D.T.Chavchich, M.Dracinsky, M.Janeba, Z.Naesens, L.Edstein, M.D.Guddat, L.W.Hockova, D.

(2017) J Med Chem 60: 7539-7554

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00926
  • Primary Citation of Related Structures:  
    5W8V

  • PubMed Abstract: 

    Acyclic nucleoside bisphosphonates (ANbPs) have previously been shown to be good inhibitors of human hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and Plasmodium falciparum (Pf) hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPRT). On the basis of this scaffold, a new series of ANbPs was synthesized. One of these new ANbPs, [3-(guanine-9-yl)-2-((2-phosphonoethoxy)methyl)propoxy]methylphosphonic acid, exhibited K i values of 6 and 70 nM for human HGPRT and Pf HGXPRT, respectively. These low K i values were achieved by inserting an extra carbon atom in the linker connecting the N 9 atom of guanine to one of the phosphonate groups. The crystal structure of this ANbP in complex with human HGPRT was determined at 2.0 Å resolution and shows that it fills three key pockets in the active site. The most potent phosphoramidate prodrugs of these compounds have IC 50 values in the low micromolar range in Pf lines and low toxicity in human A549 cells, demonstrating that these ANbPs are excellent antimalarial drug leads.


  • Organizational Affiliation

    The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferase
A, B, C, D
215Homo sapiensMutation(s): 0 
Gene Names: HPRT1HPRT
EC: 2.4.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for P00492 (Homo sapiens)
Explore P00492 
Go to UniProtKB:  P00492
PHAROS:  P00492
GTEx:  ENSG00000165704 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00492
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
9YP Binding MOAD:  5W8V Ki: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.667α = 90
b = 128.399β = 102.98
c = 65.326γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1030353
Czech Science FoundationCzech Republic16-06049S
Institute of Organic Chemistry and BiochemistryCzech RepublicRVO 61388963
Gilead SciencesCzech RepublicFoster City, USA

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Database references
  • Version 2.0: 2024-03-13
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations