Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56550.95 
• Atom Count: 3966 
• Residue Count: 512 
• Unique protein chains: 1

3AI8

Cathepsin B in complex with the nitroxoline

• DOI: 10.2210/pdb3AI8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• 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 
• R-Value Work: 0.183 

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: 10.1002/cmdc.201100098

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cathepsin B	B, A	256	Homo sapiens	Mutation(s): 0  Gene Names: CTSB (CPSB) EC: 3.4.22.1
Find proteins for P07858 (Homo sapiens) Go to Gene View: CTSB Go to UniProtKB:  P07858

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
HNQ	Ki: 39500 - 271800 nM (100) BINDINGDB
HNQ	Ki: 271800 nM BINDINGMOAD
HNQ	Ki: 154400 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 153.682	α = 90.00
b = 29.976	β = 126.25
c = 119.198	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-11 
• 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
  Type: Version format compliance
• Version 1.2: 2014-01-29
  Type: Database references