3AI8

Cathepsin B in complex with the nitroxoline

• PDB DOI: https://doi.org/10.2210/pdb3AI8/pdb

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


• Deposited: 2010-05-11 Released: 2011-05-18 
• Deposition Author(s): Renko, M., Mirkovic, B., Gobec, S., Kos, J., Turk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.244 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Novel mechanism of cathepsin B inhibition by antibiotic nitroxoline and related compounds

Mirkovic, B., Renko, M., Turk, S., Sosic, I., Jevnikar, Z., Obermajer, N., Turk, D., Gobec, S., Kos, J.

(2011) ChemMedChem 6: 1351-1356

• PubMed: 21598397 
• DOI: https://doi.org/10.1002/cmdc.201100098
• Primary Citation of Related Structures:  
  3AI8

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Organizational Affiliation: 

Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.55 kDa 
• Atom Count: 4,250 
• Modelled Residue Count: 512 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A [auth B], B [auth A]	256	Homo sapiens	Mutation(s): 0  Gene Names: CTSB EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens) Explore P07858  Go to UniProtKB:  P07858
PHAROS:  P07858 GTEx:  ENSG00000164733

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HNQ	C [auth B], D [auth A]	5-nitroquinolin-8-ol C9 H6 N2 O3 RJIWZDNTCBHXAL-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HNQ	BindingDB:  3AI8	Ki: min: 3.95e+4, max: 2.72e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.244 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.682	α = 90
b = 29.976	β = 126.25
c = 119.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Renko, M., Mirkovic, B., Gobec, S., Kos, J., Turk, D.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-29
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary