7PR9

Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor VL166

  • Classification: HYDROLASE
  • Organism(s): Burkholderia pseudomallei K96243
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-09-21 Released: 2022-08-03 
  • Deposition Author(s): Wu, L., Armstrong, Z., Davies, G.J.
  • Funding Organization(s): European Research Council (ERC), Netherlands Organisation for Scientific Research (NWO), Israel Science Foundation, European Molecular Biology Organization (EMBO), Royal Society, Wellcome Trust

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo.

de Boer, C.Armstrong, Z.Lit, V.A.J.Barash, U.Ruijgrok, G.Boyango, I.Weitzenberg, M.M.Schroder, S.P.Sarris, A.J.C.Meeuwenoord, N.J.Bule, P.Kayal, Y.Ilan, N.Codee, J.D.C.Vlodavsky, I.Overkleeft, H.S.Davies, G.J.Wu, L.

(2022) Proc Natl Acad Sci U S A 119: e2203167119-e2203167119

  • DOI: 10.1073/pnas.2203167119
  • Primary Citation of Related Structures:  
    7PR6, 7PR7, 7PR8, 7PR9, 7PRB, 7PRT, 7PSH, 7PSI, 7PSJ, 7PSK

  • PubMed Abstract: 
  • Heparan sulfate proteoglycans (HSPGs) mediate essential interactions throughout the extracellular matrix (ECM), providing signals that regulate cellular growth and development. Altered HSPG composition during tumorigenesis strongly aids cancer progression ...

    Heparan sulfate proteoglycans (HSPGs) mediate essential interactions throughout the extracellular matrix (ECM), providing signals that regulate cellular growth and development. Altered HSPG composition during tumorigenesis strongly aids cancer progression. Heparanase (HPSE) is the principal enzyme responsible for extracellular heparan sulfate catabolism and is markedly up-regulated in aggressive cancers. HPSE overactivity degrades HSPGs within the ECM, facilitating metastatic dissemination and releasing mitogens that drive cellular proliferation. Reducing extracellular HPSE activity reduces cancer growth, but few effective inhibitors are known, and none are clinically approved. Inspired by the natural glycosidase inhibitor cyclophellitol, we developed nanomolar mechanism-based, irreversible HPSE inhibitors that are effective within physiological environments. Application of cyclophellitol-derived HPSE inhibitors reduces cancer aggression in cellulo and significantly ameliorates murine metastasis. Mechanism-based irreversible HPSE inhibition is an unexplored anticancer strategy. We demonstrate the feasibility of such compounds to control pathological HPSE-driven malignancies.


    Organizational Affiliation

    The Rosalind Franklin Institute, Harwell, OX11 0FA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyco_hydro_44 domain-containing proteinA, B438Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSL2070
UniProt
Find proteins for Q63T97 (Burkholderia pseudomallei (strain K96243))
Explore Q63T97 
Go to UniProtKB:  Q63T97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63T97
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acidC, D 2N/AN/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.87α = 90
b = 104.137β = 90
c = 113.988γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomERC-2011-AdG-290836
European Research Council (ERC)United KingdomERC-2012-AdG-322942
Netherlands Organisation for Scientific Research (NWO)United Kingdom--
Israel Science FoundationUnited Kingdom1021/19
European Molecular Biology Organization (EMBO)United KingdomSTF8184
Royal SocietyUnited Kingdom--
Wellcome TrustUnited Kingdom218579/Z/19/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release