2FQ9 | pdb_00002fq9

Cathepsin S with nitrile inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.212 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.190 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Cathepsin S with nitrile inhibitor

Somoza, J.R.

To be published.

Macromolecule Content 

  • Total Structure Weight: 50.99 kDa 
  • Atom Count: 3,665 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 450 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cathepsin S
A, B
225Homo sapiensMutation(s): 0 
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
CRJ

Query on CRJ


Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]		N-(1-CYANOCYCLOPROPYL)-3-({[(2S)-5-OXOPYRROLIDIN-2-YL]METHYL}SULFONYL)-N~2~-[(1S)-2,2,2-TRIFLUORO-1-(4-FLUOROPHENYL)ETH YL]-L-ALANINAMIDE
C20 H22 F4 N4 O4 S
JLPXDVXMMYRTKN-ZOBUZTSGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.212 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.190 (DCC) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.239α = 90
b = 85.239β = 90
c = 150.966γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2006-03-21 
    • Deposition Author(s): Somoza, J.R.

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary