5F02

CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro-pyridin-2-yl)-azetidine-3-carbonyl]-pyrrolidine-2-carboxylic acid (1-cyano-cyclopropyl)-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Real-World Perspective on Molecular Design.

Kuhn, B.Guba, W.Hert, J.Banner, D.Bissantz, C.Ceccarelli, S.Haap, W.Korner, M.Kuglstatter, A.Lerner, C.Mattei, P.Neidhart, W.Pinard, E.Rudolph, M.G.Schulz-Gasch, T.Woltering, T.Stahl, M.

(2016) J.Med.Chem. 59: 4087-4102

  • DOI: 10.1021/acs.jmedchem.5b01875
  • Primary Citation of Related Structures:  
  • Also Cited By: 6DMI

  • PubMed Abstract: 
  • We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts ...

    We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.


    Organizational Affiliation

    Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin L1
A
220Homo sapiensMutation(s): 0 
Gene Names: CTSL (CTSL1)
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Go to Gene View: CTSL
Go to UniProtKB:  P07711
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5T9
Query on 5T9

Download SDF File 
Download CCD File 
A
(2~{S},4~{R})-4-[(2-chloranyl-4-methoxy-phenyl)-bis(oxidanyl)-$l^{4}-sulfanyl]-1-[3-(5-chloranylpyridin-2-yl)azetidin-3-yl]carbonyl-~{N}-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide
C25 H29 Cl2 N5 O5 S
FIOCGZWDGDSHLA-LPHCSBGTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.937α = 90.00
b = 57.492β = 90.00
c = 75.691γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references