8E07

Crystal structure of HPSE P6 in complex with triose pentosan inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Complex Inhibitory Mechanism of Glycomimetics with Heparanase.

Whitefield, C.Vo, Y.Schwartz, B.D.Hepburn, C.Ahmed, F.H.Onagi, H.Banwell, M.G.Nelms, K.Malins, L.R.Jackson, C.J.

(2023) Biochemistry 62: 2202-2215

  • DOI: https://doi.org/10.1021/acs.biochem.3c00038
  • Primary Citation of Related Structures:  
    8E07, 8E08

  • PubMed Abstract: 

    Heparanase (HPSE) is the only mammalian endo -β-glucuronidase known to catalyze the degradation of heparan sulfate. Dysfunction of HPSE activity has been linked to several disease states, resulting in HPSE becoming the target of numerous therapeutic programs, yet no drug has passed clinical trials to date. Pentosan polysulfate sodium (PPS) is a heterogeneous, FDA-approved drug for the treatment of interstitial cystitis and a known HPSE inhibitor. However, due to its heterogeneity, characterization of its mechanism of HPSE inhibition is challenging. Here, we show that inhibition of HPSE by PPS is complex, involving multiple overlapping binding events, each influenced by factors such as oligosaccharide length and inhibitor-induced changes in the protein secondary structure. The present work advances our molecular understanding of the inhibition of HPSE and will aid in the development of therapeutics for the treatment of a broad range of pathologies associated with enzyme dysfunction, including cancer, inflammatory disease, and viral infections.


  • Organizational Affiliation

    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparanase 50 kDa subunit387Homo sapiensMutation(s): 26 
Gene Names: HPSEHEPHPAHPA1HPR1HPSE1HSE1
EC: 3.2.1.166
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y251 (Homo sapiens)
Explore Q9Y251 
Go to UniProtKB:  Q9Y251
PHAROS:  Q9Y251
GTEx:  ENSG00000173083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y251
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heparanase 8 kDa subunit92Homo sapiensMutation(s): 0 
Gene Names: HPSEHEPHPAHPA1HPR1HPSE1HSE1
EC: 3.2.1.166
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y251 (Homo sapiens)
Explore Q9Y251 
Go to UniProtKB:  Q9Y251
PHAROS:  Q9Y251
GTEx:  ENSG00000173083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y251
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,3,4-tri-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranose-(1-4)-2,3-di-O-sulfo-beta-D-xylopyranoseC,
D [auth F]
3N/AN/A
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NH4
Query on NH4

Download Ideal Coordinates CCD File 
H [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.536α = 90
b = 76.195β = 90
c = 124.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaLP160101552

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Structure summary