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- PDB-1yt7: Cathepsin K complexed with a constrained ketoamide inhibitor -

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Basic information

Entry
Database: PDB / ID: 1yt7
TitleCathepsin K complexed with a constrained ketoamide inhibitor
ComponentsCathepsin K
KeywordsHYDROLASE / cathepsin / cysteine protease
Function / homology
Function and homology information


cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / Collagen degradation / fibronectin binding / collagen catabolic process / mitophagy / extracellular matrix disassembly / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / immune response / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / nucleoplasm
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-3FC / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBarrett, D.G. / Boncek, V.M. / Catalano, J.G. / Deaton, D.N. / Hassell, A.M. / Jurgensen, C.H. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. ...Barrett, D.G. / Boncek, V.M. / Catalano, J.G. / Deaton, D.N. / Hassell, A.M. / Jurgensen, C.H. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. / Payne, J.A. / Ray, J.A. / Samano, V. / Shewchuk, L.M. / Tavares, F.X. / Wells-Knecht, K.J. / Willard, D.H. / Wright, L.L. / Zhou, H.Q.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: P(2)-P(3) conformationally constrained ketoamide-based inhibitors of cathepsin K.
Authors: Barrett, D.G. / Boncek, V.M. / Catalano, J.G. / Deaton, D.N. / Hassell, A.M. / Jurgensen, C.H. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. / Payne, J.A. / Ray, J.A. / Samano, ...Authors: Barrett, D.G. / Boncek, V.M. / Catalano, J.G. / Deaton, D.N. / Hassell, A.M. / Jurgensen, C.H. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. / Payne, J.A. / Ray, J.A. / Samano, V. / Shewchuk, L.M. / Tavares, F.X. / Wells-Knecht, K.J. / Willard, D.H. / Wright, L.L. / Zhou, H.Q.
History
DepositionFeb 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2994
Polymers23,5231
Non-polymers7763
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.645, 65.645, 34.467
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Cathepsin K / Cathepsin O / Cathepsin X / Cathepsin O2


Mass: 23523.480 Da / Num. of mol.: 1 / Fragment: sequence database residues 115-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43235, cathepsin K
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3FC / (1R)-2,2-DIMETHYL-1-({5-[4-(TRIFLUOROMETHYL)PHENYL]-1,3,4-OXADIAZOL-2-YL}METHYL)PROPYL (1S)-1-{OXO[(2-OXO-1,3-OXAZOLIDIN-3-YL)AMINO]ACETYL}PENTYLCARBAMATE


Mass: 583.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32F3N5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.86 Å3/Da / Density % sol: 31.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M AMMONIUM SULFATE, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 25, 2001
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→18.24 Å / Num. all: 7170 / Num. obs: 7078 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 8.8 / Num. unique all: 1003 / % possible all: 91.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q6K

1q6k


Resolution: 2.3→18 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: mask method used for bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.251 770 -random
Rwork0.183 ---
all-7170 --
obs-7078 96 %-
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å21.54 Å20 Å2
2---2.61 Å20 Å2
3---5.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 51 105 1790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.328 119 -
Rwork0.233 --
obs-1003 91.1 %

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