4K69

Crystal Structure of Human Chymase in Complex with Fragment Linked Benzimidazolone Inhibitor: (3S)-3-{3-[(6-bromo-2-oxo-2,3-dihydro-1H-indol-4-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}hexanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.


    Related Citations: 
    • Benzimidazolone as potent chymase inhibitor: modulation of reactive metabolite formation in the hydrophobic (P1) region.
      Lo, H.Y.,Nemoto, P.A.,Kim, J.M.,Hao, M.H.,Qian, K.C.,Farrow, N.A.,Albaugh, D.R.,Fowler, D.M.,Schneiderman, R.D.,Michael August, E.,Martin, L.,Hill-Drzewi, M.,Pullen, S.S.,Takahashi, H.,De Lombaert, S.
      (2011) Bioorg.Med.Chem.Lett. 21: 4533


    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
1P9
Query on 1P9

Download SDF File 
Download CCD File 
A
(3S)-3-{3-[(6-bromo-2-oxo-2,3-dihydro-1H-indol-4-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}hexanoic acid
C22 H22 Br N3 O4
HGSJUJNYFCUFGB-HNNXBMFYSA-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 %)
1P9IC50: 40 nM (98) BINDINGDB
1P9IC50: 40 nM BINDINGMOAD
1P9IC50: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 74.365α = 90.00
b = 74.365β = 90.00
c = 49.474γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHENIXrefinement
d*TREKdata scaling

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