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- PDB-9o2i: Heparanase P6 in complex with fragment C2 -

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Basic information

Entry
Database: PDB / ID: 9o2i
TitleHeparanase P6 in complex with fragment C2
Components
  • Heparanase 50 kDa subunit
  • Heparanase 8 kDa subunit
KeywordsHYDROLASE / Heparanase / small molecule / cancer / complex / therapeutics
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process ...heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process / vascular wound healing / protein transmembrane transport / establishment of endothelial barrier / angiogenesis involved in wound healing / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / lysosomal lumen / cell-matrix adhesion / extracellular matrix / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / intracellular membrane-bounded organelle / lysosomal membrane / response to antibiotic / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, L.J. / Frkic, R.L. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Fragment Screening and Structure-Guided Development of Heparanase Inhibitors Reveal Orthosteric and Allosteric Inhibition
Authors: Davies, L.J. / Whitefield, C. / Kim, H. / Nitsche, C. / Jackson, C.J. / Frkic, R.L.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparanase 50 kDa subunit
B: Heparanase 8 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5544
Polymers51,2602
Non-polymers2942
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-74 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.962, 74.668, 124.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heparanase 50 kDa subunit


Mass: 42986.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y251
#2: Protein Heparanase 8 kDa subunit


Mass: 8273.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y251
#3: Chemical ChemComp-AUM / [nitroso(phosphonomethyl)amino]acetic acid


Mass: 198.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N2O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M ammonium acetate, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→47.83 Å / Num. obs: 19657 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.948 / Rmerge(I) obs: 0.603 / Rpim(I) all: 0.174 / Rrim(I) all: 0.628 / Χ2: 1 / Net I/σ(I): 5.2 / Num. measured all: 251445
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 98.9 % / Redundancy: 13 % / Rmerge(I) obs: 1.856 / Num. measured all: 27927 / Num. unique obs: 2156 / CC1/2: 0.351 / Rpim(I) all: 0.531 / Rrim(I) all: 1.932 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.83 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 975 4.97 %
Rwork0.2179 --
obs0.2205 19602 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 17 128 3765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.507
X-RAY DIFFRACTIONf_dihedral_angle_d13.5971371
X-RAY DIFFRACTIONf_chiral_restr0.04554
X-RAY DIFFRACTIONf_plane_restr0.004645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.3911400.32332602X-RAY DIFFRACTION100
2.63-2.80.32281420.28862617X-RAY DIFFRACTION100
2.8-3.010.34141290.2632618X-RAY DIFFRACTION100
3.01-3.320.28251480.22032621X-RAY DIFFRACTION100
3.32-3.80.24791280.18232664X-RAY DIFFRACTION100
3.8-4.780.19761370.15442699X-RAY DIFFRACTION100
4.79-47.830.23521510.20562806X-RAY DIFFRACTION100

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