5MQY

CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors.

Kuhn, B.Tichy, M.Wang, L.Robinson, S.Martin, R.E.Kuglstatter, A.Benz, J.Giroud, M.Schirmeister, T.Abel, R.Diederich, F.Hert, J.

(2017) J Med Chem 60: 2485-2497

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01881
  • Primary Citation of Related Structures:  
    5MQY

  • PubMed Abstract: 

    Improving the binding affinity of a chemical series by systematically probing one of its exit vectors is a medicinal chemistry activity that can benefit from molecular modeling input. Herein, we compare the effectiveness of four approaches in prioritizing building blocks with better potency: selection by a medicinal chemist, manual modeling, docking followed by manual filtering, and free energy calculations (FEP). Our study focused on identifying novel substituents for the apolar S2 pocket of cathepsin L and was conducted entirely in a prospective manner with synthesis and activity determination of 36 novel compounds. We found that FEP selected compounds with improved affinity for 8 out of 10 picks compared to 1 out of 10 for the other approaches. From this result and other additional analyses, we conclude that FEP can be a useful approach to guide this type of medicinal chemistry optimization once it has been validated for the system under consideration.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin L1220Homo sapiensMutation(s): 0 
Gene Names: CTSLCTSL1
EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
PHAROS:  P07711
GTEx:  ENSG00000135047 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07711
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GH4
Query on GH4

Download Ideal Coordinates CCD File 
B [auth A]4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile
C21 H19 F N4 O3
WKKCNOKGPKWFJS-FOKLQQMPSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.907α = 90
b = 57.2β = 90
c = 75.735γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary