4K2Y

Crystal Structure of Human Chymase in Complex with Fragment Inhibitor 6-chloro-1,3-dihydro-2H-indol-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Potent, Selective Chymase Inhibitors via Fragment Linking Strategies.

Taylor, S.J.Padyana, A.K.Abeywardane, A.Liang, S.Hao, M.H.De Lombaert, S.Proudfoot, J.Farmer, B.S.Li, X.Collins, B.Martin, L.Albaugh, D.R.Hill-Drzewi, M.Pullen, S.S.Takahashi, H.

(2013) J.Med.Chem. 56: 4465-4481

  • DOI: 10.1021/jm400138z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chymase plays an important and diverse role in the homeostasis of a number of cardiovascular processes. Herein, we describe the identification of potent, selective chymase inhibitors, developed using fragment-based, structure-guided linking and optim ...

    Chymase plays an important and diverse role in the homeostasis of a number of cardiovascular processes. Herein, we describe the identification of potent, selective chymase inhibitors, developed using fragment-based, structure-guided linking and optimization techniques. High-concentration biophysical screening methods followed by high-throughput crystallography identified an oxindole fragment bound to the S1 pocket of the protein exhibiting a novel interaction pattern hitherto not observed in chymase inhibitors. X-ray crystallographic structures were used to guide the elaboration/linking of the fragment, ultimately leading to a potent inhibitor that was >100-fold selective over cathepsin G and that mitigated a number of liabilities associated with poor physicochemical properties of the series it was derived from.


    Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877-0368, USA. steven.taylor@boehringeringelheim.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chymase
A
226Homo sapiensMutation(s): 0 
Gene Names: CMA1 (CYH, CYM)
EC: 3.4.21.39
Find proteins for P23946 (Homo sapiens)
Go to Gene View: CMA1
Go to UniProtKB:  P23946
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ES2
Query on ES2

Download SDF File 
Download CCD File 
A
6-chloro-1,3-dihydro-2H-indol-2-one
C8 H6 Cl N O
CENVPIZOTHULGJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ES2IC50: 470000 nM (98) BINDINGDB
ES2IC50: 470000 nM BINDINGMOAD
ES2IC50: 470000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.178 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 74.405α = 90.00
b = 74.405β = 90.00
c = 49.701γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSphasing
d*TREKdata reduction
d*TREKdata scaling
PHENIXrefinement
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references
  • Version 1.2: 2019-07-17
    Type: Advisory, Data collection, Derived calculations, Refinement description