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- PDB-5mqy: CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-pheno... -

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Basic information

Entry
Database: PDB / ID: 5mqy
TitleCATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile
ComponentsCathepsin L1
KeywordsHYDROLASE / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / Collagen degradation / protein autoprocessing / fibronectin binding / collagen catabolic process / serpin family protein binding / collagen binding / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / Degradation of the extracellular matrix / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / adaptive immune response / histone binding / Attachment and Entry / lysosome / apical plasma membrane / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-GH4 / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsKuglstatter, A. / Stihle, M. / Benz, J.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors.
Authors: Kuhn, B. / Tichy, M. / Wang, L. / Robinson, S. / Martin, R.E. / Kuglstatter, A. / Benz, J. / Giroud, M. / Schirmeister, T. / Abel, R. / Diederich, F. / Hert, J.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Data collection
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,08310
Polymers24,1921
Non-polymers8919
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint20 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.907, 57.200, 75.735
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 Cathepsin L1 / Cathepsin L / Major excreted protein / MEP


Mass: 24191.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL, CTSL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07711, cathepsin L
#2: Chemical ChemComp-GH4 / 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile


Mass: 394.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19FN4O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→39.26 Å / Num. obs: 75222 / % possible obs: 99.8 % / Redundancy: 6.15 % / Rmerge(I) obs: 0.0428 / Rsym value: 0.0428 / Net I/σ(I): 13.65
Reflection shellResolution: 1.13→1.23 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.04 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDS(VERSION May 1 2016)data reduction
Aimlessdata scaling
REFMAC5.8.0155refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F02

5f02


Resolution: 1.13→39.26 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.018 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.038
RfactorNum. reflection% reflectionSelection details
Rfree0.19898 3712 5 %RANDOM
Rwork0.14869 ---
obs0.15105 71261 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.934 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å20 Å2
2--0.23 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.13→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 61 251 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0191803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7921.9652433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79425.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6815278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.933156
X-RAY DIFFRACTIONr_chiral_restr0.1970.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0211408
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.9661.906878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.342.871099
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0232.294925
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.77730.0363199
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.69731803
X-RAY DIFFRACTIONr_sphericity_free30.698578
X-RAY DIFFRACTIONr_sphericity_bonded18.39451931
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 256 -
Rwork0.35 5180 -
obs--99.38 %

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