1GMY

Cathepsin B complexed with dipeptidyl nitrile inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Identification of Dipeptidyl Nitriles as Potent and Selective Inhibitors of Cathepsin B Through Structure-Based Drug Design

Greenspan, P.D.Clark, K.L.Tommasi, R.A.Cowen, S.D.Mcquire, L.W.Farley, D.L.Van Duzer, J.H.Goldberg, R.L.Zhou, H.Du, Z.Fitt, J.J.Coppa, D.E.Fang, Z.Macchia, W.Zhu, L.Capparelli, M.P.Goldstein, R.Wigg, A.M.Doughty, J.R.S Bohacek, R.Knap, A.K.

(2001) J.Med.Chem. 44: 4524


  • PubMed Abstract: 
  • Cathepsin B is a member of the papain superfamily of cysteine proteases and has been implicated in the pathology of numerous diseases, including arthritis and cancer. As part of an effort to identify potent, reversible inhibitors of this protease, we ...

    Cathepsin B is a member of the papain superfamily of cysteine proteases and has been implicated in the pathology of numerous diseases, including arthritis and cancer. As part of an effort to identify potent, reversible inhibitors of this protease, we examined a series of dipeptidyl nitriles, starting with the previously reported Cbz-Phe-NH-CH(2)CN (19, IC(50) = 62 microM). High-resolution X-ray crystallographic data and molecular modeling were used to optimize the P(1), P(2), and P(3) substituents of this template. Cathepsin B is unique in its class in that it contains a carboxylate recognition site in the S(2)' pocket of the active site. Inhibitor potency and selectivity were enhanced by tethering a carboxylate functionality from the carbon alpha to the nitrile to interact with this region of the enzyme. This resulted in the identification of compound 10, a 7 nM inhibitor of cathepsin B, with excellent selectivity over other cysteine cathepsins.


    Organizational Affiliation

    Arthritis and Bone Metabolism Research, Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901, USA. paul.greenspan@pharma.novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATHEPSIN B
A, B, C
261Homo sapiensGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AEM
Query on AEM

Download SDF File 
Download CCD File 
A, B, C
2-AMINOETHANIMIDIC ACID
C2 H6 N2
AXQVKDQRBAXYBP-HNQUOIGGSA-N
 Ligand Interaction
APD
Query on APD

Download SDF File 
Download CCD File 
A, B, C
3-METHYLPHENYLALANINE
C10 H13 N O2
JZRBSTONIYRNRI-VIFPVBQESA-N
 Ligand Interaction
DFA
Query on DFA

Download SDF File 
Download CCD File 
A, B, C
DIPHENYLACETIC ACID
C14 H12 O2
PYHXGXCGESYPCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.900α = 90.00
b = 103.900β = 90.00
c = 125.600γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2002-09-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection