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- PDB-8jyg: Crystal structure of Human HPSE1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8jyg
TitleCrystal structure of Human HPSE1 in complex with inhibitor
Components
  • Heparanase
  • Heparanase 50 kDa subunit
KeywordsHYDROLASE/INHIBITOR / Endo-glucoronidase / Heparanase-1 / HEP / HPA / HPA1 / HPR1 / HPSE1 / HSE1 / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport / syndecan binding / vascular wound healing / angiogenesis involved in wound healing / establishment of endothelial barrier / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / 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
Chem-V8R / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMima, M. / Fujimoto, N. / Imai, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem. / Year: 2023
Title: Structure-based lead optimization to improve potency and selectivity of a novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid series of heparanase-1 inhibitor.
Authors: Imai, Y. / Suzuki, R. / Wakasugi, D. / Matsuda, D. / Tanaka-Yamamoto, N. / Ohki, Y. / Mima, M. / Endo, M. / Tabata, R. / Matsuzawa, H. / Hasegawa, Y. / Kato, S. / Sugisaki, M. / Miyagawa, H. ...Authors: Imai, Y. / Suzuki, R. / Wakasugi, D. / Matsuda, D. / Tanaka-Yamamoto, N. / Ohki, Y. / Mima, M. / Endo, M. / Tabata, R. / Matsuzawa, H. / Hasegawa, Y. / Kato, S. / Sugisaki, M. / Miyagawa, H. / Fujimoto, N. / Fukunaga, T. / Kato, S. / Takahashi, T. / Kakinuma, H.
History
DepositionJul 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,09827
Polymers51,8802
Non-polymers2,21825
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint5 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.380, 71.049, 78.280
Angle α, β, γ (deg.)90.000, 98.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Heparanase 50 kDa subunit


Mass: 43464.074 Da / Num. of mol.: 1 / Mutation: K307R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase
#2: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 8415.670 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase

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Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 231 molecules

#3: Chemical ChemComp-V8R / (5~{S},6~{R},7~{S},8~{S})-6,7,8-tris(oxidanyl)-2-[2-(3-phenoxyphenyl)ethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid


Mass: 410.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→77.5 Å / Num. obs: 32623 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.993 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2388 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E8M
Resolution: 2→43.977 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.914 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2092 1600 4.907 %
Rwork0.1656 31005 -
all0.168 --
obs-32605 99.807 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.783 Å2
Baniso -1Baniso -2Baniso -3
1--0.678 Å20 Å21.313 Å2
2---3.109 Å2-0 Å2
3---3.282 Å2
Refinement stepCycle: LAST / Resolution: 2→43.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 146 208 3998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133862
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153750
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6755193
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5958628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75121.823181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57915643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0871522
X-RAY DIFFRACTIONr_chiral_restr0.070.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
X-RAY DIFFRACTIONr_nbd_refined0.2010.2790
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23614
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21860
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21856
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2206
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.222
X-RAY DIFFRACTIONr_nbd_other0.2170.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2340.211
X-RAY DIFFRACTIONr_mcbond_it2.5933.1811838
X-RAY DIFFRACTIONr_mcbond_other2.573.1771837
X-RAY DIFFRACTIONr_mcangle_it3.9354.7572294
X-RAY DIFFRACTIONr_mcangle_other3.9394.7612295
X-RAY DIFFRACTIONr_scbond_it3.23.6052024
X-RAY DIFFRACTIONr_scbond_other3.1993.6062025
X-RAY DIFFRACTIONr_scangle_it4.9485.2212899
X-RAY DIFFRACTIONr_scangle_other4.9485.2222900
X-RAY DIFFRACTIONr_lrange_it8.65161.46217654
X-RAY DIFFRACTIONr_lrange_other8.65161.44817643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2731340.2542254X-RAY DIFFRACTION99.7911
2.052-2.1080.2511150.2342233X-RAY DIFFRACTION99.6604
2.108-2.1690.2291030.2252144X-RAY DIFFRACTION99.6011
2.169-2.2360.2581100.2082109X-RAY DIFFRACTION99.7303
2.236-2.3090.2391150.1962012X-RAY DIFFRACTION99.953
2.309-2.390.228970.1811989X-RAY DIFFRACTION99.9521
2.39-2.480.2511010.1831930X-RAY DIFFRACTION99.8525
2.48-2.5810.2151050.1661802X-RAY DIFFRACTION99.8952
2.581-2.6960.23850.161750X-RAY DIFFRACTION99.4041
2.696-2.8280.25830.1611693X-RAY DIFFRACTION99.7753
2.828-2.980.229810.1591607X-RAY DIFFRACTION99.7047
2.98-3.1610.205850.1611510X-RAY DIFFRACTION100
3.161-3.3790.235720.1681424X-RAY DIFFRACTION99.9332
3.379-3.6490.172700.1461332X-RAY DIFFRACTION99.8576
3.649-3.9960.201610.1441228X-RAY DIFFRACTION99.9225
3.996-4.4660.125510.1241117X-RAY DIFFRACTION100
4.466-5.1540.147410.123986X-RAY DIFFRACTION99.9027
5.154-6.3060.204350.168861X-RAY DIFFRACTION100
6.306-8.8880.212380.155648X-RAY DIFFRACTION99.8544
8.888-43.9770.157180.151376X-RAY DIFFRACTION99.7468

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