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⇱ RCSB PDB - 1YK7: Cathepsin K complexed with a cyanopyrrolidine inhibitor

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 1YK7 | pdb_00001yk7

Cathepsin K complexed with a cyanopyrrolidine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.270 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.199 (DCC) 

Starting Model: experimental
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wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Novel and potent cyclic cyanamide-based cathepsin K inhibitors.

Deaton, D.N., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Tavares, F.X., Willard, D.H., Wright, L.L.

(2005) Bioorg Med Chem Lett 15: 1815-1819

  • DOI: https://doi.org/10.1016/j.bmcl.2005.02.033
  • Primary Citation Related Structures: 
    1YK7

  • PubMed Abstract: 

    Starting from a PDE IV inhibitor hit derived from high throughput screening of the compound collection, a key pyrrolidine cyanamide pharmacophore was identified. Modifications of the pyrrolidine ring produced enhancements in cathepsin K inhibition. An X-ray co-crystal structure of a cyanamide with cathepsin K confirmed the mode of inhibition.

    • Organizational Affiliation: 
    • Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA. david.n.deaton@gsk.com

Macromolecule Content 

  • Total Structure Weight: 23.88 kDa 
  • Atom Count: 1,782 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 215 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
Gene Names: CTSK, CTSO, CTSO2
EC: 3.4.22.38
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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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NBL

Query on NBL


Download:Ideal Coordinates CCD File
B [auth A]N2-[(BENZYLOXY)CARBONYL]-N1-[(3S)-1-CYANOPYRROLIDIN-3-YL]-L-LEUCINAMIDE
C19 H26 N4 O3
IMTUSTXBVIALBC-SJORKVTESA-N		👁 Image

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.270 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.241α = 90
b = 66.653β = 90
c = 93.187γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.