Cathepsin K
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain X； UniProt 115–329 | Fragment：full length Mutation：wild type | ORH 3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.4；298 K；30%(W/V) PEG 4000 and 150 mM Ammonium Sulfate pH 3.4 3 microliter of protein at 10 mg/ml and 2 microliter of reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K | Resolution 2.02 Å R-free 0.263 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain Y； UniProt 115–329 | Fragment：full length Mutation：wild type | ORH 3,5-dioxo-4-(3-piperidin-1-ylpropyl)-2-[3-(trifluoromethyl)phenyl]-2,3,4,5-tetrahydro-1,2,4-triazine-6-carbonitrile × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.4；298 K；30%(W/V) PEG 4000 and 150 mM Ammonium Sulfate pH 3.4 3 microliter of protein at 10 mg/ml and 2 microliter of reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K | Resolution 2.02 Å R-free 0.263 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 3KWB | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1ATK CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64 Deposited 1996-12-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.2；PROTEIN CRYSTALLIZED FROM 10% PEG 8000, 0.1 M NA/K PHOSPHATE AT PH 6.2 CONTAINING 0.2 M NACL AT ROOM TEMPERATURE BY VAPOR DIFFUSION., vapor diffusion
|
Resolution 2.20 Å R-free 0.310 |
| 1AU0 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT SYMMETRIC DIACYLAMINOMETHYL KETONE INHIBITOR Deposited 1997-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | SDK 1,3-BIS[[N-[(PHENYLMETHOXY)CARBONYL]-L-LEUCYL]AMINO]-2-PROPANONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.2；10% ISOPROPANOL,0.1M NAPO4-CITRATE, PH4.2
|
Resolution 2.60 Å R-free 0.365 |
| 1AU2 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PROPANONE INHIBITOR Deposited 1997-09-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | POS 1-[[(4-PHENOXYPHENYL)SULFONYL]AMINO]-3-[[N/N-(4-PYRIDINYLCARBONYL)-L-LEUCYL]AMINO]-2-PROPANOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.5；18% PEG 8000, 0.12M LI2SO4, 0.06M SODIUM ACETATE, PH 4.5
|
Resolution 2.60 Å R-free 0.333 |
| 1AU3 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PYRROLIDINONE INHIBITOR Deposited 1997-09-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | PCM 1-[N[(PHENYLMETHOXY)CARBONYL]-L-LEUCYL-4-[[N/N-[(PHENYLMETHOXY)CARBONYL]-/NL-LEUCYL]AMINO]-3-PYRROLIDINONE/N × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；28% MPD, 0.1M MES, 0.1M TRIS-HCL, PH 7.0
|
Resolution 2.50 Å R-free 0.353 |
| 1AU4 CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PYRROLIDINONE INHIBITOR Deposited 1997-09-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | INP 4-[[N-[(PHENYLMETHOXY)CARBONYL]-/NL/N-LEUCYL]AMINO]-1[(2S)-2-[[[4-(PYRIDINYLMETHOXY)CARBONYL]AMINO]-4-METHYLPENT/NYL]-3-PYRROLIDINONE/N × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；30% MPD, 0.1M MES, 0.1M TRIS, PH 7.0
|
Resolution 2.30 Å R-free 0.370 |
| 1AYU CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT SYMMETRIC BISCARBOHYDRAZIDE INHIBITOR Deposited 1997-11-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | INA 1,5-BIS(N-BENZYLOXYCARBONYL-L-LEUCINYL)CARBOHYDRAZIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；30% MPD, 0.1M MES, 0.1M TRIS-HCL, PH7.0
|
Resolution 2.20 Å R-free 0.318 |
| 1AYV CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT THIAZOLHYDRAZIDE INHIBITOR Deposited 1997-11-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | IN6 N-[2-[1-(N-BENZYLOXYCARBONYLAMINO)-3-METHYLBUTYL]THIAZOL-4-YLCARBONYL]-N'-(BENZYLOXYCARBONYL-L-LEUCINYL)HYDRAZIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；30% MPD, 0.1M MES, 0.1M TRIS-HCL, PH7.0
|
Resolution 2.30 Å R-free 0.312 |
| 1AYW CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT BENZYLOXYBENZOYLCARBOHYDRAZIDE INHIBITOR Deposited 1997-11-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | IN3 1-(N-BENZYLOXYCARBONYL-L-LEUCINYL)-5-(3-BENZYLOXY BENZOYL)CARBOHYDRAZIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.5；22.5% PEG 8000, 0.075M SODIUM ACETATE, 0.15M LITHIUM ACETATE, PH4.5
|
Resolution 2.40 Å R-free 0.379 |
| 1BGO CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR Deposited 1998-05-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | I10 1-[2-(3-BIPHENYL)-4-METHYLVALERYL)]AMINO-3-(2-PYRIDYLSULFONYL)AMINO-2-PROPANONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.5；pH 4.5
|
Resolution 2.30 Å R-free 0.296 |
| 1BY8 THE CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN K Deposited 1998-10-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
16–329（314 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5；8-10 % PEG 6000, 0.1M NA CITRATE, PH 5.0
|
Resolution 2.60 Å R-free 0.344 |
| 1MEM Crystal structure of Cathepsin K complexed with a potent vinyl sulfone inhibitor Deposited 1997-01-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | 0D6 N-{(1R)-3-phenyl-1-[2-(phenylsulfonyl)ethyl]propyl}-N~2~-(piperazin-1-ylcarbonyl)-L-leucinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；MG FORMATE, UNBUFFERED, pH 6.0
|
Resolution 1.80 Å |
| 1NL6 Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A Covalent Azepanone Inhibitor Deposited 2003-01-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | 750 5-(2-MORPHOLIN-4-YLETHOXY)BENZOFURAN-2-CARBOXYLIC ACID ((S)-3-METHYL-1-{(S)-3-OXO-1-[2-(3-PYRIDIN-2-YLPHENYL)ACETYL]AZEPAN-4-YLCARBAMOYL}BUTYL)AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；10% PEG 8000, 0.1 M imidazole, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.298 |
| 1NL6 Crystal Structure Of The Cysteine Protease Human Cathepsin K In Complex With A Covalent Azepanone Inhibitor Deposited 2003-01-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
115–329（215 aa）
|
Not recorded | 750 5-(2-MORPHOLIN-4-YLETHOXY)BENZOFURAN-2-CARBOXYLIC ACID ((S)-3-METHYL-1-{(S)-3-OXO-1-[2-(3-PYRIDIN-2-YLPHENYL)ACETYL]AZEPAN-4-YLCARBAMOYL}BUTYL)AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；10% PEG 8000, 0.1 M imidazole, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.298 |
| 1NLJ CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT AZEPANONE INHIBITOR Deposited 2003-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | 2CA BENZOFURAN-2-CARBOXYLIC ACID {(S)-3-METHYL-1-[3-OXO-1-(PYRIDIN-2-YLSULFONYL)AZEPAN-4-YLCARBAMOYL]BUTYL}AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% MPD, 0.1 M MES,0.1 M tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.295 |
| 1NLJ CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT AZEPANONE INHIBITOR Deposited 2003-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
115–329（215 aa）
|
Not recorded | 2CA BENZOFURAN-2-CARBOXYLIC ACID {(S)-3-METHYL-1-[3-OXO-1-(PYRIDIN-2-YLSULFONYL)AZEPAN-4-YLCARBAMOYL]BUTYL}AMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；30% MPD, 0.1 M MES,0.1 M tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.295 |
| 1Q6K Cathepsin K complexed with t-butyl(1S)-1-cyclohexyl-2-oxoethylcarbamate Deposited 2003-08-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | SO4 SULFATE ION × 1 TCO TERT-BUTYL(1S)-1-CYCLOHEXYL-2-OXOETHYLCARBAMATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；0.2 M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.10 Å |
| 1SNK Cathepsin K complexed with carbamate derivatized norleucine aldehyde Deposited 2004-03-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–329（214 aa）
|
Not recorded | SO4 SULFATE ION × 3 MYE N2-({[(4-BROMOPHENYL)METHYL]OXY}CARBONYL)-N1-[(1S)-1-FORMYLPENTYL]-L-LEUCINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；295 K；0.2M ammonium sulfate, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50
|
Resolution 2.40 Å R-free 0.286 |
| 1TU6 Cathepsin K complexed with a ketoamide inhibitor Deposited 2004-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
Fragment：cathepsin K: mature form (residues 115-329)
Chain B
115–329（215 aa）
Fragment：cathepsin K: mature form (residues 115-329)
|
Not recorded | SO4 SULFATE ION × 3 FSP [1-(4-FLUOROBENZYL)CYCLOBUTYL]METHYL (1S)-1-[OXO(1H-PYRAZOL-5-YLAMINO)ACETYL]PENTYLCARBAMATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.75 Å R-free 0.214 |
| 1U9V Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABE854 Deposited 2004-08-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
113–329（217 aa）
|
Not recorded | IHE 6-(CYCLOHEXYLAMINO)-9-[2-(4-METHYLPIPERAZIN-1-YL)-ETHYL]-9H-PURINE-2-CARBONITRILE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；PEG 4000, Tris, magnesium chloride, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.231 |
| 1U9W Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABI491 Deposited 2004-08-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
113–329（217 aa）
|
Not recorded | IHI 9-CYCLOPENTYL-6-[2-(3-IMIDAZOL-1-YL-PROPOXY)-PHENYLAMINO]-9H-PURINE-2-CARBONITRILE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, Tris, Lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.226 |
| 1U9X Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABJ688 Deposited 2004-08-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
113–329（217 aa）
|
Not recorded | IHJ 9-CYCLOPENTYL-6-{2-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPOXY]-PHENYLAMINO}-9H-PURINE-2-CARBONITRILE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；sodium citrate, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.217 |
| 1VSN Crystal structure of a potent small molecule inhibitor bound to cathepsin K Deposited 2007-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：cathepsin K
|
Not recorded | NFT N-(2-AMINOETHYL)-N~2~-{(1S)-1-[4'-(AMINOSULFONYL)BIPHENYL-4-YL]-2,2,2-TRIFLUOROETHYL}-L-LEUCINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Mg formate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.209 |
| 1YK7 Cathepsin K complexed with a cyanopyrrolidine inhibitor Deposited 2005-01-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：mature form of cathepsin K (sequence database residues 115-329)
|
Not recorded | NBL N2-[(BENZYLOXY)CARBONYL]-N1-[(3S)-1-CYANOPYRROLIDIN-3-YL]-L-LEUCINAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.270 |
| 1YK8 Cathepsin K complexed with a cyanamide-based inhibitor Deposited 2005-01-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：sequence database residues 115-329
|
Not recorded | T2M TERT-BUTYL 2-CYANO-2-METHYLHYDRAZINECARBOXYLATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.277 |
| 1YT7 Cathepsin K complexed with a constrained ketoamide inhibitor Deposited 2005-02-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：sequence database residues 115-329
|
Not recorded | SO4 SULFATE ION × 2 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 × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2M AMMONIUM SULFATE, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.251 |
| 2ATO Crystal structure of Human Cathepsin K in complex with myocrisin Deposited 2005-08-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | SO4 SULFATE ION × 1 MYQ (S)-(1,2-DICARBOXYETHYLTHIO)GOLD × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；22% MPD, 100 mM acetate buffer, 20 mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.198 |
| 2AUX Cathepsin K complexed with a semicarbazone inhibitor Deposited 2005-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：mature form of cathepsin K (residues 115-329)
|
Not recorded | CT1 (1R)-2-METHYL-1-(PHENYLMETHYL)PROPYL[(1S)-1-FORMYLPENTYL]CARBAMATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；0.2 M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.40 Å R-free 0.253 |
| 2AUZ Cathepsin K complexed with a semicarbazone inhibitor Deposited 2005-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：mature form of cathepsin K (residues 115-329)
|
Not recorded | SO4 SULFATE ION × 3 CT2 1-(PHENYLMETHYL)CYCLOPENTYL[(1S)-1-FORMYLPENTYL]CARBAMATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；0.2M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.30 Å R-free 0.239 |
| 2BDL Cathepsin K complexed with a pyrrolidine ketoamide-based inhibitor Deposited 2005-10-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：mature form of cathepsin K (residues 115-329)
|
Not recorded | 4PR (3S)-1-{[(3,5-DIMETHYLISOXAZOL-4-YL)AMINO]CARBONYL}-4,4-DIMETHYLPYRROLIDIN-3-YL{(1S)-1-[1-HYDROXY-2-OXO-2-{[(1R)-1-PHENYLETHYL]AMINO}ETHYL]PENTYL}CARBAMATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.2 M ammonium sulfate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.00 Å R-free 0.241 |
| 2R6N Crystal structure of a pyrrolopyrimidine inhibitor in complex with human Cathepsin K Deposited 2007-09-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
113–329（217 aa）
|
Not recorded | CKE 1-{7-cyclohexyl-6-[4-(4-methylpiperazin-1-yl)benzyl]-7H-pyrrolo[2,3-d]pyrimidin-2-yl}methanamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；20 % PEG 4000, 10 % Isopropanol, 0.1 M HEPES pH 7.5, vapor diffusion, hanging drop, temperature 298K
|
Resolution 1.95 Å R-free 0.184 |
| 3C9E Crystal structure of the cathepsin K : chondroitin sulfate complex. Deposited 2008-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
|
Not recorded | CA CALCIUM ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Cathepsin K:chondroitin sulfate complex was made at 1:1 ratio. Precipitant contained
30% MPD, 0.1M sodium acetate buffer, 20mM calcium chloride, pH 4.5, VAPOR DIFFUSION,
HANGING DROP, temperature 295K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.80 Å R-free 0.209 |
| 3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Mutation：K9E, I171E, Q172S, N190M, K191G, L195K | CA CALCIUM ION × 1 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.24 Å R-free 0.238 |
| 3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
115–329（215 aa）
Fragment：UNP residues 115-329
|
Mutation：K9E, I171E, Q172S, N190M, K191G, L195K | CA CALCIUM ION × 1 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.24 Å R-free 0.238 |
| 3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Mutation：K9E, I171E, Q172S, N190M, K191G, L195K | CA CALCIUM ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.24 Å R-free 0.238 |
| 3H7D The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate Deposited 2009-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
115–329（215 aa）
Fragment：UNP residues 115-329
|
Mutation：K9E, I171E, Q172S, N190M, K191G, L195K | CA CALCIUM ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.24 Å R-free 0.238 |
| 3KW9 X-ray structure of Cathepsin K covalently bound to a triazine ligand Deposited 2009-12-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115 to 329
|
Not recorded | ORG 4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile × 1 TFA trifluoroacetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 2.9；298 K；30% PEG4000, 0.2M Ammoniumsulphate pH2.9
cryoprotectant:
crystallisation solution + 10% PEG4000
, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.259 |
| 3KWZ Cathepsin K in complex with a non-selective 2-cyano-pyrimidine inhibitor Deposited 2009-12-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Not recorded | SO4 SULFATE ION × 6 KWZ 4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.4；26% PEG 4000, 0.1M Tris, 0.2M LiSO4, 15% PEG 400, pH 8.4, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.49 Å R-free 0.299 |
| 3KX1 Cathepsin K in complex with a selective 2-cyano-pyrimidine inhibitor Deposited 2009-12-02 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Not recorded | KX1 4-cycloheptyl-6-(3-piperidin-1-ylpropyl)pyrimidine-2-carbonitrile × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 2.9；34% PEG 4000, 0.2M ammonium sulphate pH 2.9, 4% methanol
, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.51 Å R-free 0.306 |
| 3O0U Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG Deposited 2010-07-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP Residues 115-329
|
Not recorded | O47 3-{2-[(E)-iminomethyl]-6-propylpyrimidin-4-yl}-N,N-dimethyl-5-(trifluoromethyl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.9；298 K；8% PEG 4K, 0.2 M Ammonium Sulfate pH=3.9, 4%
Methanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.80 Å R-free 0.217 |
| 3O1G Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group. Deposited 2010-07-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | SO4 SULFATE ION × 2 O75 N-benzyl-3-(2-cyano-6-propylpyrimidin-4-yl)-N-[2-(dimethylamino)ethyl]-5-(trifluoromethyl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.4；298 K；Cocrystallization. Protein solution: 20 mM NaAcetate pH 4.0, 0.2 M NaCl. Crystallization condition: 32% PEG 4K, 0.1 M Tris pH 8.4, 0.2 M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.65 Å R-free 0.198 |
| 3OVZ Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead Deposited 2010-09-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
121–329（209 aa）
Fragment：UNP residues 121-329
|
Not recorded | O96 N-[(1S)-3-amino-1-ethyl-2,3-dioxopropyl]-2-chloro-4-(pyridin-2-ylmethoxy)-3-(trifluoromethyl)benzamide × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
298 K；0 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20%
PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K
|
Resolution 2.02 Å R-free 0.308 |
| 4DMX Cathepsin K inhibitor Deposited 2012-02-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：unp residues 115-329
|
Not recorded | 0LB (1R,2R)-N-(1-cyanocyclopropyl)-2-{[4-(4-fluorophenyl)piperazin-1-yl]carbonyl}cyclohexanecarboxamide × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；293 K；PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K
|
Resolution 1.70 Å R-free 0.206 |
| 4DMY Cathepsin K inhibitor Deposited 2012-02-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：unp residues 115-329
|
Not recorded | 0LC (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；293 K；PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K
|
Resolution 1.63 Å R-free 0.190 |
| 4DMY Cathepsin K inhibitor Deposited 2012-02-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
115–329（215 aa）
Fragment：unp residues 115-329
|
Not recorded | 0LC (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；293 K；PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K
|
Resolution 1.63 Å R-free 0.190 |
| 4N79 Structure of Cathepsin K-dermatan sulfate complex Deposited 2013-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；VAPOR DIFFUSION
|
Resolution 2.62 Å R-free 0.260 |
| 4N8W cathepsin K - chondroitin sulfate complex Deposited 2013-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.5；290 K；24% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate and 100 mM calcium chloride, pH 4.5, VAPOR DIFFUSION, temperature 290K
|
Resolution 2.02 Å R-free 0.176 |
| 4X6H Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. Deposited 2014-12-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Not recorded | 3XT 4-amino-3-fluoro-N-(1-{[(2Z)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide × 1 I37 4-amino-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}-3-fluorobenzamide × 1 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；0.1 M Tri-Sodium Citrate, 2.4 M Ammonium Sulfate
|
Resolution 1.00 Å R-free 0.166 |
| 4X6I Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. Deposited 2014-12-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP RESIDUES 115-329
|
Not recorded | 3Y1 2-amino-4-bromo-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}benzamide × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；Lithium sulfate 0.2M,
Sodium acetate 0.1M,
Peg 8000 30%
|
Resolution 1.87 Å R-free 0.237 |
| 4X6J Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. Deposited 2014-12-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP RESIDUES 115-329
|
Not recorded | GOL GLYCEROL × 1 CL CHLORIDE ION × 1 K POTASSIUM ION × 1 PGO S-1,2-PROPANEDIOL × 3 3Y2 2-amino-4-chloro-N-(1-{[(2E)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；Potassium chloride 0.2M,
HEPES 0.05M,
5/4 PO/OH 35%
|
Resolution 1.59 Å R-free 0.238 |
| 4YV8 Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal Deposited 2015-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Not recorded | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；24% PEG 8000, 0.2M ammonium sulfate
|
Resolution 2.00 Å R-free 0.205 |
| 4YVA Cathepsin K co-crystallized with actinomycetes extract Deposited 2015-03-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294.15 K；24% PEG 8000, 0.2M Ammonium sulfate
|
Resolution 1.80 Å R-free 0.210 |
| 5J94 Human cathepsin K mutant C25S in complex with the allosteric effector NSC13345 Deposited 2016-04-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
107–329（223 aa）
|
Mutation：C25S | 1XF 2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.2 M ammonium sulfate, 30% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.22 Å R-free 0.234 |
| 5JA7 Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914 Deposited 2016-04-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
107–329（223 aa）
|
Mutation：C25S | 6HM [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M ammonium sulfate, 30% (w/v) PEG-8000
|
Resolution 1.61 Å R-free 0.220 |
| 5JA7 Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914 Deposited 2016-04-12 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
107–329（223 aa）
|
Mutation：C25S | 6HM [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M ammonium sulfate, 30% (w/v) PEG-8000
|
Resolution 1.61 Å R-free 0.220 |
| 5JH3 Human cathepsin K mutant C25S Deposited 2016-04-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
107–329（223 aa）
|
Not recorded | SO4 SULFATE ION × 2 ACT ACETATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.2 M ammonium sulfate, 30% (w/v) PEG-8000
|
Resolution 1.75 Å R-free 0.211 |
| 5TDI Crystal structure of Cathepsin K with a covalently-linked inhibitor at 1.4 Angstrom resolution. Deposited 2016-09-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Mutation：S49A | 7AS 4-fluoro-N-{1-[(Z)-iminomethyl]cyclopropyl}-N~2~-{(1S)-2,2,2-trifluoro-1-[4'-(methylsulfonyl)[1,1'-biphenyl]-4-yl]ethyl }-L-leucinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.05 M cadmium sulfate hydrate, 0.1 M HEPES pH 7.5, 1.0 M sodium acetate trihydrate
|
Resolution 1.40 Å R-free 0.171 |
| 5TUN Crystal structure of uninhibited human Cathepsin K at 1.62 Angstrom resolution Deposited 2016-11-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；294.15 K；20% polyethylene glycol (PEG) 8000, 0.1 M phosphate/citrate pH 4.2 and 0.2 M sodium chloride
|
Resolution 1.62 Å R-free 0.195 |
| 5Z5O Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K Deposited 2018-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
16–329（314 aa）
Chain B
16–88（73 aa）
|
Mutation：C139S/I249T Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 16 SO4 SULFATE ION × 5 PEG DI(HYDROXYETHYL)ETHER × 7 CL CHLORIDE ION × 1 NA SODIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100mM Na-K Phosphate 6.2, 20 % MPD, 12mM (NH4)2SO4, 10% PEG 3350
|
Resolution 1.92 Å R-free 0.204 |
| 6ASH Crystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution Deposited 2017-08-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：UNP residues 115-329
|
Mutation：S49A | 1XF 2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；8% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate
|
Resolution 1.42 Å R-free 0.146 |
| 6HGY CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C Deposited 2018-08-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | G4B THALASSOSPIRAMIDE C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.05M MES pH 6.0, 0.1M Na-Oxalate, 0.1M CaCl2
|
Resolution 2.20 Å R-free 0.310 |
| 6PXF Structure of human Cathepsin K with an ectosteric inhibitor at 1.85 Angstrom resolution Deposited 2019-07-25 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Mutation：S49A | J0V 1,6,6-trimethyl-10,11-dioxo-6,7,8,9,10,11-hexahydrophenanthro[1,2-b]furan-2-sulfonic acid × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；0.04 M Potassium phosphate monobasic, 16% w/v PEG8000, 20% v/v glycerol
|
Resolution 1.85 Å R-free 0.188 |
| 6QBS The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K Deposited 2018-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
Chain B
115–329（215 aa）
|
Not recorded | HVW (2~{S})-4-methyl-~{N}-prop-2-enyl-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295.15 K；0.2 M CaCl2, 20 % PEG-3350
|
Resolution 1.70 Å R-free 0.210 |
| 6QL8 Cathepsin-K in complex with MIV-711 Deposited 2019-01-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
113–329（217 aa）
|
Not recorded | J5N ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-ethynyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 NO3 NITRATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100mM ADA pH6.0, 500mM ammonium nitrate, 17% PEG 3350
|
Resolution 1.80 Å R-free 0.181 |
| 6QLM Cathepsin-K in complex with MIV-701 Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
114–329（216 aa）
|
Not recorded | HFH ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 300mM NaCl & 20% PEG 5k.mme
|
Resolution 1.50 Å R-free 0.142 |
| 6QLM Cathepsin-K in complex with MIV-701 Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
114–329（216 aa）
|
Not recorded | HFH ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 MHA (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 300mM NaCl & 20% PEG 5k.mme
|
Resolution 1.50 Å R-free 0.142 |
| 6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
114–329（216 aa）
|
Not recorded | J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
|
Resolution 2.00 Å R-free 0.225 |
| 6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
114–329（216 aa）
|
Not recorded | J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
|
Resolution 2.00 Å R-free 0.225 |
| 6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
114–329（216 aa）
|
Not recorded | J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
|
Resolution 2.00 Å R-free 0.225 |
| 6QLW Cathepsin-K in complex with MIV-710 Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
114–329（216 aa）
|
Not recorded | J5T ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
|
Resolution 2.00 Å R-free 0.225 |
| 6QLX Cathepsin-K in complex with fluoro-oxa-azabicyclo[3.3.0]octanyl containing inhibitor Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
114–329（216 aa）
|
Not recorded | HKH ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-thiophen-2-yl-benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 400mM sodium chloride and 20% PEG 5k.mme
|
Resolution 2.10 Å R-free 0.237 |
| 6QM0 Cathepsin-K in complex with amino-oxaazabicyclo[3.3.0]octanyl containing inhibitor Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
114–329（216 aa）
|
Not recorded | MHA (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID × 1 J6B ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-azanyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-fluoranyl-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
|
Resolution 1.90 Å R-free 0.174 |
| 6QM0 Cathepsin-K in complex with amino-oxaazabicyclo[3.3.0]octanyl containing inhibitor Deposited 2019-02-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
114–329（216 aa）
|
Not recorded | J6B ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-azanyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-fluoranyl-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
|
Resolution 1.90 Å R-free 0.174 |
| 7NXL Structure of human cathepsin K in complex with the acrylamide inhibitor Gu3110 Deposited 2021-03-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain AAA
114–329（216 aa）
|
Not recorded | SO4 SULFATE ION × 1 UUK tert-butyl (1-((4-(dibenzylamino)-4-oxobutyl)amino)-4-methyl-1-oxopentan-2-yl)carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5.
Morpheus C4 condition
|
Resolution 1.80 Å R-free 0.209 |
| 7NXM Structure of human cathepsin K in complex with the selective activity-based probe Gu3416 Deposited 2021-03-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
114–329（216 aa）
|
Not recorded | SO4 SULFATE ION × 1 UUW N-(4-(dibenzylamino)-4-oxobutyl)-2-(5-(dimethylamino)pentanamido)-4-methylpentanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5.
Morpheus C4 condition
|
Resolution 1.72 Å R-free 0.178 |
| 7PCK CRYSTAL STRUCTURE OF WILD TYPE HUMAN PROCATHEPSIN K Deposited 1998-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
16–329（314 aa）
Chain C
16–329（314 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；100 MM TRIS-HCL, 5% 2-METHYL-2,4-PENTANEDIOL, 12 MM AMMONIUM SULPHATE AND 9% PEG, pH 7.0
|
Resolution 3.20 Å R-free 0.253 |
| 7PCK CRYSTAL STRUCTURE OF WILD TYPE HUMAN PROCATHEPSIN K Deposited 1998-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
16–329（314 aa）
Chain D
16–329（314 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；100 MM TRIS-HCL, 5% 2-METHYL-2,4-PENTANEDIOL, 12 MM AMMONIUM SULPHATE AND 9% PEG, pH 7.0
|
Resolution 3.20 Å R-free 0.253 |
| 7QBL Structure of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602 Deposited 2021-11-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
115–329（215 aa）
|
Not recorded | A0U ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；10% PEG 8000, 20% ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5
|
Resolution 2.00 Å R-free 0.286 |
| 7QBM Structure of the activation intermediate of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602 Deposited 2021-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
114–329（216 aa）
Chain P
16–89（74 aa）
|
Not recorded | A0U ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate × 1 ACT ACETATE ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；290 K；10% PEG 8000, 20% ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5
|
Resolution 1.88 Å R-free 0.234 |
| 7QBN Structure of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303 Deposited 2021-11-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
113–329（217 aa）
|
Not recorded | 9ZG (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；290 K；12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M MES/imidazole pH 6.5
|
Resolution 1.55 Å R-free 0.167 |
| 7QBO Structure of the activation intermediate of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303 Deposited 2021-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
114–329（216 aa）
Chain P
16–89（74 aa）
|
Not recorded | 9ZG (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；290 K；10% PEG 8000, 20% ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine HCl, 0.02 M DL-serine, 0.1M MES/imidazole pH 6.5
|
Resolution 1.90 Å R-free 0.212 |
| 8C3D Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections Deposited 2022-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
|
Not recorded | CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；30 % PEG-3350, 0.2 M CaCL2
|
Resolution 2.00 Å R-free 0.227 |
| 9G6A Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue Deposited 2024-07-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
115–329（215 aa）
Chain B
115–329（215 aa）
|
Not recorded | A1IJC (2~{S})-4-methyl-~{N}-(2-oxidanylidenepropyl)-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide × 2 PGE TRIETHYLENE GLYCOL × 3 CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6；293 K；20 % PEG-3350, 0.2 M CaCl2
|
Resolution 1.99 Å R-free 0.206 |
69 other PDB entries and 82 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CATK_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain X； PDBConstruct 1–215； UniProt 115–329 Author chain Y； PDBConstruct 1–215； UniProt 115–329 |
