2XU5

CATHEPSIN L WITH A NITRILE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb2XU5/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: 1.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Starting Model: other

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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.99 kDa 
• Atom Count: 1,889 
• Modelled Residue Count: 216 
• 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
XU5	B [auth A]	(2S,4R)-4-(2-chlorophenyl)sulfonyl-N-[1-(iminomethyl)cyclopropyl]-1-[1-(4-methylphenyl)cyclopropyl]carbonyl-pyrrolidine-2-carboxamide C26 H28 Cl N3 O4 S UZYJLDSLFCNNEE-NOUGMWGKSA-N
FLC	D [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XU5	PDBBind:  2XU5	IC50: 130 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.943	α = 90
b = 59.107	β = 90
c = 89.79	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: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description