1AYW | pdb_00001ayw
CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT BENZYLOXYBENZOYLCARBOHYDRAZIDE INHIBITOR
- PDB DOI: https://doi.org/10.2210/pdb1AYW/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 1997-11-10 Released: 1998-11-25
- Deposition Author(s): Zhao, B., Smith, W.W., Janson, C.A., Abdel-Meguid, S.S.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.379 (Depositor)
- R-Value Work: 0.237 (Depositor)
- R-Value Observed: 0.237 (Depositor)
Starting Model: experimental
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wwPDB Validation3D Report Full Report
Literature
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Design of potent and selective human cathepsin K inhibitors that span the active site.
Thompson, S.K., Halbert, S.M., Bossard, M.J., Tomaszek, T.A., Levy, M.A., Zhao, B., Smith, W.W., Abdel-Meguid, S.S., Janson, C.A., D'Alessio, K.J., McQueney, M.S., Amegadzie, B.Y., Hanning, C.R., DesJarlais, R.L., Briand, J., Sarkar, S.K., Huddleston, M.J., Ijames, C.F., Carr, S.A., Garnes, K.T., Shu, A., Heys, J.R., Bradbeer, J., Zembryki, D., Lee-Rykaczewski, L., James, I.E., Lark, M.W., Drake, F.H., Gowen, M., Gleason, J.G., Veber, D.F.(1997) Proc Natl Acad Sci U S A 94: 14249-14254
- PubMed: 9405598 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1073/pnas.94.26.14249
- Primary Citation Related Structures:
1AYU, 1AYV, 1AYW - PubMed Abstract:
Potent and selective active-site-spanning inhibitors have been designed for cathepsin K, a cysteine protease unique to osteoclasts. They act by mechanisms that involve tight binding intermediates, potentially on a hydrolytic pathway. X-ray crystallographic, MS, NMR spectroscopic, and kinetic studies of the mechanisms of inhibition indicate that different intermediates or transition states are being represented that are dependent on the conditions of measurement and the specific groups flanking the carbonyl in the inhibitor. The species observed crystallographically are most consistent with tetrahedral intermediates that may be close approximations of those that occur during substrate hydrolysis. Initial kinetic studies suggest the possibility of irreversible and reversible active-site modification. Representative inhibitors have demonstrated antiresorptive activity both in vitro and in vivo and therefore are promising leads for therapeutic agents for the treatment of osteoporosis. Expansion of these inhibitor concepts can be envisioned for the many other cysteine proteases implicated for therapeutic intervention.
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (IN3)
Biological Assembly 1
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (IN3)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 24.07 kDa
- Atom Count: 1,751
- Modeled Residue Count: 215
- Deposited Residue Count: 215
- Unique protein chains: 1
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| CATHEPSIN K | 215 | Homo sapiens | Mutation(s): 0 EC: 3.4.22.38 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P43235 GTEx: ENSG00000143387 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P43235 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IN3 Download:Ideal Coordinates CCD File | B [auth A] | 1-(N-BENZYLOXYCARBONYL-L-LEUCINYL)-5-(3-BENZYLOXY BENZOYL)CARBOHYDRAZIDE C29 H33 N5 O6 CEXWCIXCWCFUSI-VWLOTQADSA-N | 👁 Image | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.379 (Depositor)
- R-Value Work: 0.237 (Depositor)
- R-Value Observed: 0.237 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.68 | α = 90 |
| b = 57.68 | β = 90 |
| c = 131.12 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XENGEN | data collection |
| XENGEN | data reduction |
| X-PLOR | model building |
| X-PLOR | refinement |
| XENGEN | data scaling |
| X-PLOR | phasing |
Entry History
Deposition Data
- Released Date: 1998-11-25 Deposition Author(s): Zhao, B., Smith, W.W., Janson, C.A., Abdel-Meguid, S.S.
Revision History (Full details and data files)
- Version 1.0: 1998-11-25
Type: Initial release - Version 1.1: 2008-03-24
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2012-02-29
Changes: Database references - Version 1.4: 2018-03-07
Changes: Data collection, Other - Version 1.5: 2023-08-02
Changes: Database references, Derived calculations, Refinement description - Version 1.6: 2024-11-20
Changes: Data collection, Structure summary
