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 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin B
B, A
256Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HNQ
Query on HNQ

Download SDF File 
Download CCD File 
A, B
5-nitroquinolin-8-ol
NITROXOLINE
C9 H6 N2 O3
RJIWZDNTCBHXAL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HNQKi: 39500 - 271800 nM (100) BINDINGDB
HNQKi: 271800 nM BINDINGMOAD
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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.682α = 90.00
b = 29.976β = 126.25
c = 119.198γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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