7PR8

Crystal structure of human heparanase in complex with covalent inhibitor GR109

  • Classification: CARBOHYDRATE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): Yes 

  • 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: 1.66 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/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. 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

    Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparanase 50 kDa subunit385Homo sapiensMutation(s): 1 
Gene Names: HPSEHEPHPAHPA1HPR1HPSE1HSE1
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 subunit74Homo sapiensMutation(s): 0 
Gene Names: HPSEHEPHPAHPA1HPR1HPSE1HSE1
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
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid
D
2N/AN/A
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.49α = 90
b = 71.29β = 95.2
c = 79.07γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description