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URL: https://www.rcsb.org/structure/1Q6K

⇱ RCSB PDB - 1Q6K: Cathepsin K complexed with t-butyl(1S)-1-cyclohexyl-2-oxoethylcarbamate

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255,630
Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 1Q6K | pdb_00001q6k

Cathepsin K complexed with t-butyl(1S)-1-cyclohexyl-2-oxoethylcarbamate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 
    0.207 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 

Literature

Exploration of the P1 SAR of aldehyde cathepsin K inhibitors

Catalano, J.G., Deaton, D.N., Furfine, E.S., Hassell, A.M., McFadyen, R.B., Miller, A.B., Miller, L.R., Shewchuk, L.M., Willard, D.H., Wright, L.L.

(2004) Bioorg Med Chem Lett 14: 275-278

  • DOI: https://doi.org/10.1016/j.bmcl.2003.09.088
  • Primary Citation Related Structures: 
    1Q6K

  • PubMed Abstract: 

    The synthesis and biological activity of a series of aldehyde inhibitors of cathepsin K are reported. Exploration of the properties of the S(1) subsite with a series of alpha-amino aldehyde derivatives substituted at the P(1) position afforded compounds with cathepsin K IC(50)s between 52 microM and 15 nM.

    • Organizational Affiliation: 
    • Department of Medicinal Chemistry, GlaxoSmithKline, Five Moore Drive, Research Triangle Park, NC 27709-3398, USA.

Macromolecule Content 

  • Total Structure Weight: 23.86 kDa 
  • Atom Count: 1,813 
  • 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 OR CTSO
EC: 3.4.22.38
👁 Image
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TCO

Query on TCO


Download:Ideal Coordinates CCD File
C [auth A]TERT-BUTYL(1S)-1-CYCLOHEXYL-2-OXOETHYLCARBAMATE
C13 H23 N O3
BDSGOSWEKUGHOV-LLVKDONJSA-N		👁 Image
SO4

Query on SO4


Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		👁 Image

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work:  0.207 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.443α = 90
b = 56.443β = 90
c = 130.212γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

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: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-02-14
    Changes: Experimental preparation
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-10-30
    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.