3OHI

Structure of Giardia fructose-1,6-biphosphate aldolase in complex with 3-hydroxy-2-pyridone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rational design, synthesis and evaluation of first generation inhibitors of the Giardia lamblia fructose-1,6-biphosphate aldolase.

Li, Z.Liu, Z.Cho, D.W.Zou, J.Gong, M.Breece, R.M.Galkin, A.Li, L.Zhao, H.Maestas, G.D.Tierney, D.L.Herzberg, O.Dunaway-Mariano, D.Mariano, P.S.

(2010) J Inorg Biochem 105: 509-517

  • DOI: 10.1016/j.jinorgbio.2010.12.012
  • Primary Citation of Related Structures:  
    3OHI

  • PubMed Abstract: 
  • Inhibitors of the Giardia lamblia fructose 1,6-bisphosphate aldolase (GlFBPA), which transforms fructose 1,6-bisphosphate (FBP) to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, were designed based on 3-hydroxy-2-pyridone and 1,2-dihydroxypyridine scaffolds that position two negatively charged tetrahedral groups for interaction with substrate phosphate binding residues, a hydrogen bond donor to the catalytic Asp83, and a Zn(2+) binding group ...

    Inhibitors of the Giardia lamblia fructose 1,6-bisphosphate aldolase (GlFBPA), which transforms fructose 1,6-bisphosphate (FBP) to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, were designed based on 3-hydroxy-2-pyridone and 1,2-dihydroxypyridine scaffolds that position two negatively charged tetrahedral groups for interaction with substrate phosphate binding residues, a hydrogen bond donor to the catalytic Asp83, and a Zn(2+) binding group. The inhibition activities for the GlFBPA catalyzed reaction of FBP of the prepared alkyl phosphonate/phosphate substituted 3-hydroxy-2-pyridinones and a dihydroxypyridine were determined. The 3-hydroxy-2-pyridone inhibitor 8 was found to bind to GlFBPA with an affinity (K(i)=14μM) that is comparable to that of FBP (K(m)=2μM) or its inert analog TBP (K(i)=1μM). The X-ray structure of the GlFBPA-inhibitor 8 complex (2.3Å) shows that 8 binds to the active site in the manner predicted by in silico docking with the exception of coordination with Zn(2+). The observed distances and orientation of the pyridone ring O=C-C-OH relative to Zn(2+) are not consistent with a strong interaction. To determine if Zn(2+)coordination occurs in the GlFBPA-inhibitor 8 complex in solution, EXAFS spectra were measured. A four coordinate geometry comprised of the three enzyme histidine ligands and an oxygen atom from the pyridone ring O=C-C-OH was indicated. Analysis of the Zn(2+) coordination geometries in recently reported structures of class II FBPAs suggests that strong Zn(2+) coordination is reserved for the enediolate-like transition state, accounting for minimal contribution of Zn(2+) coordination to binding of 8 to GlFBPA.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative fructose-1,6-bisphosphate aldolaseA, B323Giardia intestinalisMutation(s): 0 
Gene Names: aldFBPA
EC: 4.1.2.13
UniProt
Find proteins for O97447 (Giardia intestinalis)
Explore O97447 
Go to UniProtKB:  O97447
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDX (Subject of Investigation/LOI)
Query on HDX

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]({3-hydroxy-2-oxo-4-[2-(phosphonooxy)ethyl]pyridin-1(2H)-yl}methyl)phosphonic acid
C8 H13 N O9 P2
RMAJJEZWSTVCSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HDX PDBBind:  3OHI Ki: 1.40e+4 (nM) from 1 assay(s)
Binding MOAD:  3OHI Ki: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.58α = 90
b = 64.95β = 90
c = 171.45γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata 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: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance