Staphylococcus aureus 7,8-Dihydro-6-hydroxymethylpterin- pyrophosphokinase in complex with AMPCPP and an inhibitor

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives as Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase from Staphylococcus Aureus.

Dennis, M.L.Chhabra, S.Wang, Z.Debono, A.Dolezal, O.Newman, J.Pitcher, N.P.Rahmani, R.Cleary, B.Barlow, N.Hattarki, M.Graham, B.Peat, T.S.Baell, J.B.Swarbrick, J.D.

(2014) J Med Chem 57: 9612

  • DOI: https://doi.org/10.1021/jm501417f
  • Primary Citation of Related Structures:  
    4CRJ, 4CWB, 4CYU

  • PubMed Abstract: 

    6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), an enzyme from the folate biosynthesis pathway, catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin and is a yet-to-be-drugged antimicrobial target. Building on our previous discovery that 8-mercaptoguanine (8MG) is an inhibitor of Staphylococcus aureus HPPK (SaHPPK), we have identified and characterized the binding of an S8-functionalized derivative (3). X-ray structures of both the SaHPPK/3/cofactor analogue ternary and the SaHPPK/cofactor analogue binary complexes have provided insight into cofactor recognition and key residues that move over 30 Å upon binding of 3, whereas NMR measurements reveal a partially plastic ternary complex active site. Synthesis and binding analysis of a set of analogues of 3 have identified an advanced new lead compound (11) displaying >20-fold higher affinity for SaHPPK than 8MG. A number of these exhibited low micromolar affinity for dihydropteroate synthase (DHPS), the adjacent, downstream enzyme to HPPK, and may thus represent promising new leads to bienzyme inhibitors.

  • Organizational Affiliation

    Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE161Staphylococcus aureusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
X6L BindingDB:  4CWB Kd: min: 810, max: 2.15e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.817α = 90
b = 83.817β = 90
c = 52.04γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description