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- PDB-9rfx: Crystal structure of Endothiapepsin in complex with follow-up com... -

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Basic information

Entry
Database: PDB / ID: 9rfx
TitleCrystal structure of Endothiapepsin in complex with follow-up compound EOS71605 from ECBL
ComponentsEndothiapepsin
KeywordsHYDROLASE / crystallographic fragment screening / Endothiapepsin / ECBL-96 fragment library
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsWollenhaupt, J. / Benz, L.S. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission871037European Union
CitationJournal: Rsc Med Chem / Year: 2025
Title: From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.
Authors: Benz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
History
DepositionJun 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2445
Polymers33,8141
Non-polymers4304
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.220, 73.360, 52.420
Angle α, β, γ (deg.)90.00, 109.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-A1JFU / 2-[3,5-bis(fluoranyl)phenoxy]-2-methyl-propan-1-amine


Mass: 201.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13F2NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 29 % (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate, pH 4.6
Time: 2-3 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→42.75 Å / Num. obs: 129789 / % possible obs: 97.9 % / Redundancy: 4.37 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.074 / Net I/σ(I): 10.26
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.161.088198190.4871.2551
1.16-1.240.715196340.7150.8091
1.24-1.340.474184370.8610.5351
1.34-1.470.27170660.9450.3071
1.47-1.640.148155040.9830.1671
1.64-1.90.087136960.9940.0971
1.9-2.320.054115940.9960.0621
2.32-3.280.04290170.9970.0481
3.28-42.750.03550220.9980.0391

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→42.72 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.501 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16848 1102 1.1 %RANDOM
Rwork0.15503 ---
obs0.15518 103822 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0.17 Å2
2--0.11 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.18→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 28 280 2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132543
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172235
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.6373508
X-RAY DIFFRACTIONr_angle_other_deg1.5961.5725190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25624.88184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.74915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.795151
X-RAY DIFFRACTIONr_chiral_restr0.0980.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023003
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02557
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0211.0561366
X-RAY DIFFRACTIONr_mcbond_other1.021.0551364
X-RAY DIFFRACTIONr_mcangle_it1.4921.5911717
X-RAY DIFFRACTIONr_mcangle_other1.4931.5911718
X-RAY DIFFRACTIONr_scbond_it1.751.1791177
X-RAY DIFFRACTIONr_scbond_other1.7491.1831178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3871.7181781
X-RAY DIFFRACTIONr_long_range_B_refined3.27113.5592794
X-RAY DIFFRACTIONr_long_range_B_other3.15113.1982743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 80 -
Rwork0.231 7554 -
obs--97.75 %

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