2XU4

CATHEPSIN L WITH A NITRILE INHIBITOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions.

Hardegger, L.A., Kuhn, B., Spinnler, B., Anselm, L., Ecabert, R., Stihle, M., Gsell, B., Thoma, R., Diez, J., Benz, J., Plancher, J.M., Hartmann, G., Banner, D.W., Haap, W., Diederich, F.

(2011) Angew Chem Int Ed Engl 50: 314


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATHEPSIN L1220Homo sapiensMutation(s): 0 
EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
PHAROS:  P07711
GTEx:  ENSG00000135047 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07711
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DJT
Query on DJT
Download Ideal Coordinates CCD File 
B [auth A](2S,4R)-4-(2-chlorophenyl)sulfonyl-1-[1-(4-fluorophenyl)cyclopropyl]carbonyl-N-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide
C25 H25 Cl F N3 O4 S
ZYXXDTSBKAWETF-OIRADOGLSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DJT PDBBind:  2XU4 IC50: 340 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.362α = 90
b = 85.362β = 90
c = 50.212γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing

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: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary