1YT7 | pdb_00001yt7

Cathepsin K complexed with a constrained ketoamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.251 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.190 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3FCClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

P(2)-P(3) conformationally constrained ketoamide-based inhibitors of cathepsin K.

Barrett, D.G.Boncek, V.M.Catalano, J.G.Deaton, D.N.Hassell, A.M.Jurgensen, C.H.Long, S.T.McFadyen, R.B.Miller, A.B.Miller, L.R.Payne, J.A.Ray, J.A.Samano, V.Shewchuk, L.M.Tavares, F.X.Wells-Knecht, K.J.Willard, D.H.Wright, L.L.Zhou, H.Q.

(2005) Bioorg Med Chem Lett 15: 3540-3546

  • DOI: https://doi.org/10.1016/j.bmcl.2005.05.062
  • Primary Citation of Related Structures:  
    1YT7

  • PubMed Abstract: 

    An orally bioavailable series of ketoamide-based cathepsin K inhibitors with good pharmacokinetic properties has been identified. Starting from a potent inhibitor endowed with poor drug properties, conformational constraint of the P(2)-P(3) linker and modifications to P(1') elements led to an enhancement in potency, solubility, clearance, and bioavailability. These optimized inhibitors attenuated bone resorption in a rat TPTX hypocalcemic bone resorption model.


  • Organizational Affiliation

    Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin K215Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43235
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3FC
Query on 3FC

Download Ideal Coordinates CCD File 
D [auth A](1R)-2,2-DIMETHYL-1-({5-[4-(TRIFLUOROMETHYL)PHENYL]-1,3,4-OXADIAZOL-2-YL}METHYL)PROPYL (1S)-1-{OXO[(2-OXO-1,3-OXAZOLIDIN-3-YL)AMINO]ACETYL}PENTYLCARBAMATE
C26 H32 F3 N5 O7
IXXKXSFSQVTOKQ-ZWKOTPCHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
3FC BindingDB:  1YT7 IC50: min: 0.13, max: 130 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.251 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.645α = 90
b = 65.645β = 90
c = 34.467γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3FCClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-19
    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: 2024-11-13
    Changes: Structure summary