2R9M

Cathepsin S complexed with Compound 15

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Design and Synthesis of Reversible Inhibitors of Cathepsin S: alpha,alpha-Disubstitution at the P1 Residue Provides Potent Inhibitors in Cellular Assays and In Vivo Models of Antigen Presentation

Ward, Y.D., Emmanuel, M.J., Thomson, D.S., Liu, W., Bekkali, Y., Frye, L.L., Girardot, M., Morwick, T., Young, E.R.R., Zindell, R., Hrapchak, M., DeTuri, M., White, A., Crane, K.M., White, D.M., Wang, Y., Hao, M.-H., Grygon, C.A., Labadia, M.E., Wildeson, J., Freeman, D., Nelson, R., Capolino, A., Peterson, J.D., Raymond, E.L., Brown, M.L., Spero, D.M.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin S
A, B
222Homo sapiensMutation(s): 0 
Gene Names: CTSS
EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens)
Explore P25774 
Go to UniProtKB:  P25774
PHAROS:  P25774
GTEx:  ENSG00000163131 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y11
Query on Y11
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-[(1S)-2-[(4-cyano-1-methylpiperidin-4-yl)amino]-1-(cyclohexylmethyl)-2-oxoethyl]morpholine-4-carboxamide
C21 H35 N5 O3
IRSOCWQJNYLTDD-SFHVURJKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Y11 PDBBind:  2R9M IC50: 1.5 (nM) from 1 assay(s)
BindingDB:  2R9M IC50: min: 0.9, max: 1.5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.273α = 90
b = 85.273β = 90
c = 150.331γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description