2R6N

Crystal structure of a pyrrolopyrimidine inhibitor in complex with human Cathepsin K

• PDB DOI: https://doi.org/10.2210/pdb2R6N/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-09-06 Released: 2007-11-06 
• Deposition Author(s): Cowan-Jacob, S.W., Ramage, P., Mathis, B., Geisse, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.184 
• R-Value Work: 0.156 

Literature

Novel scaffold for cathepsin K inhibitors.

Teno, N., Miyake, T., Ehara, T., Irie, O., Sakaki, J., Ohmori, O., Gunji, H., Matsuura, N., Masuya, K., Hitomi, Y., Nonomura, K., Horiuchi, M., Gohda, K., Iwasaki, A., Umemura, I., Tada, S., Kometani, M., Iwasaki, G., Cowan-Jacob, S.W., Missbach, M., Lattmann, R., Betschart, C.

(2007) Bioorg Med Chem Lett 17: 6096-6100

• PubMed: 17911019 
• DOI: https://doi.org/10.1016/j.bmcl.2007.09.047
• Primary Citation of Related Structures:  
  2R6N


• PubMed Abstract: 
  

  Pyrrolopyrimidine, a novel scaffold, allows to adjust interactions within the S3 subsite of cathepsin K. The core intermediate 10 facilitated the P3 optimization and identified highly potent and selective cathepsin K inhibitors 11-20.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Ohkubo 8, Tsukuba, Ibaraki, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.16 kDa 
• Atom Count: 1,906 
• Modelled Residue Count: 216 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	217	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CKE	B [auth A]	1-{7-cyclohexyl-6-[4-(4-methylpiperazin-1-yl)benzyl]-7H-pyrrolo[2,3-d]pyrimidin-2-yl}methanamine C25 H34 N6 GCJSOJRPNOWSEH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CKE	PDBBind:  2R6N	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.184 
• R-Value Work: 0.156 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.4	α = 90
b = 62.4	β = 90
c = 121.8	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Cowan-Jacob, S.W., Ramage, P., Mathis, B., Geisse, S.

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2024-10-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary