2XU3

CATHEPSIN L WITH A NITRILE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb2XU3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-14 Released: 2011-01-12 
• Deposition Author(s): Banner, D.W., Benz, J.M., Haap, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 0.155 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 

Starting Model: experimental

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

• PubMed: 21184410 
• DOI: https://doi.org/10.1002/anie.201006781
• Primary Citation of Related Structures:  
  2XU1, 2XU3, 2XU4, 2XU5

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Organizational Affiliation: 

Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.19 kDa 
• Atom Count: 2,324 
• Modelled Residue Count: 220 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATHEPSIN L1	A	220	Homo sapiens	Mutation(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
GTEx:  ENSG00000135047

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XU3	B [auth A]	(2S,4R)-4-(2-chlorophenyl)sulfonyl-1-[1-(5-chlorothiophen-2-yl)cyclopropyl]carbonyl-N-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide C23 H23 Cl2 N3 O4 S2 UKVPZPACPGTUIO-UPJLJTPPSA-N
BTB	C [auth A], E [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
XU3	PDBBind:  2XU3	IC50: 160 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 0.155 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.441	α = 90
b = 49.394	β = 105.13
c = 46.129	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Banner, D.W., Benz, J.M., Haap, W.

Revision History  

• 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: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description