4CRJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/jm501417f
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE (HPPK)
A
161N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download SDF File 
Download CCD File 
A
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
YH5
Query on YH5

Download SDF File 
Download CCD File 
A
2-amino-8-{[2-(4-methoxyphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one
C14 H13 N5 O3 S
SQNJCPSJSYBCFC-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YH5Kd: 1090 - 76600 nM (99) BINDINGDB
YH5Kd: 1100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 82.480α = 90.00
b = 82.480β = 90.00
c = 52.173γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Atomic model, Derived calculations, Non-polymer description
  • Version 1.2: 2019-05-08
    Type: Data collection, Experimental preparation, Other