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- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
3O0U|pdb_00003o0u
Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG
- PDB DOI: https://doi.org/10.2210/pdb3O0U/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No
- Deposited: 2010-07-20 Released: 2011-03-30
- Deposition Author(s): Fradera, X.,van Zeeland, M.,Uitdehaag, J.C.M.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.217 (Depositor), 0.210 (DCC)
- R-Value Work: 0.152 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.155 (Depositor)
Starting Model:other
View more details
Download MendeleyOptimisation of 2-cyano-pyrimidine inhibitors of cathepsin K: improving selectivity over hERG.
Rankovic, Z., Cai, J., Kerr, J., Fradera, X., Robinson, J., Mistry, A., Finlay, W., McGarry, G., Andrews, F., Caulfield, W., Cumming, I., Dempster, M., Waller, J., Arbuckle, W., Anderson, M., Martin, I., Mitchell, A., Long, C., Baugh, M., Westwood, P., Kinghorn, E., Jones, P., Uitdehaag, J.C., van Zeeland, M., Potin, D., Saniere, L., Fouquet, A., Chevallier, F., Deronzier, H., Dorleans, C., Nicolai, E.(2010) Bioorg Med Chem Lett 20: 6237-6241
- PubMed: 20843687 Search on PubMed
- DOI: https://doi.org/10.1016/j.bmcl.2010.08.101
- Primary Citation of Related Structures:
3O0U,3O1G - PubMed Abstract:
Several structure-guided optimisation strategies were explored in order to improve the hERG selectivity profile of cathepsin K inhibitor 1, whilst maintaining its otherwise excellent in vitro and in vivo profile. Ultimately, attenuation of clogP and pK(a) properties proved a successful approach and led to the discovery of a potent analogue 23, which, in addition to the desired selectivity over hERG (>1000-fold), displayed a highly attractive overall profile.
Organizational Affiliation:
Merck Research Laboratories, MSD, Newhouse, Lanarkshire, ML1 5SH Scotland, United Kingdom. zoran.rankovic@merck.com
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (O47)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 23.89 kDa
- Atom Count: 1,877
- Modelled Residue Count: 215
- Deposited Residue Count: 215
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cathepsin K | 215 | Homo sapiens | Mutation(s): 0 Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P43235 (Homo sapiens) Explore P43235 Go to UniProtKB: P43235 | |||||
PHAROS: P43235 GTEx: ENSG00000143387 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P43235 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| O47 Query on O47 Download Ideal Coordinates CCD File | B [auth A] | 3-{2-[(E)-iminomethyl]-6-propylpyrimidin-4-yl}-N,N-dimethyl-5-(trifluoromethyl)benzamide C18 H19 F3 N4 O FLPAOFVJMBOQGB-LSHDLFTRSA-N |  | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.217 (Depositor), 0.210 (DCC)
- R-Value Work: 0.152 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.155 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 37.695 | α = 90 |
| b = 48.967 | β = 90 |
| c = 103.958 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CrystalClear | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
Deposition Data
- Released Date: 2011-03-30 Deposition Author(s): Fradera, X.,van Zeeland, M.,Uitdehaag, J.C.M.
Revision History (Full details and data files)
- Version 1.0: 2011-03-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2024-11-27
Changes: Structure summary
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