3AI8

Cathepsin B in complex with the nitroxoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin BAB256Homo sapiensMutation(s): 0 
Gene Names: CTSBCPSB
EC: 3.4.22.1
Find proteins for P07858 (Homo sapiens)
Explore P07858 
Go to UniProtKB:  P07858
NIH Common Fund Data Resources
PHAROS  P07858
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HNQ
Query on HNQ

Download CCD File 
A, B
5-nitroquinolin-8-ol
C9 H6 N2 O3
RJIWZDNTCBHXAL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HNQKi:  271800   nM  Binding MOAD
HNQKi:  39500   nM  BindingDB
HNQKi:  154400   nM  BindingDB
HNQKi:  271800   nM  BindingDB
HNQKi :  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 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.682α = 90
b = 29.976β = 126.25
c = 119.198γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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