4K5Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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:  
    4K2Y, 4K69, 4K5Z, 4K60

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ChymaseA226Homo sapiensMutation(s): 0 
Gene Names: CMA1CYHCYM
EC: 3.4.21.39
Find proteins for P23946 (Homo sapiens)
Explore P23946 
Go to UniProtKB:  P23946
NIH Common Fund Data Resources
PHAROS  P23946
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
1P7
Query on 1P7

Download CCD File 
A
6-chloro-2,3-dihydro-1H-isoindol-1-one
C8 H6 Cl N O
VCEOKEOSVQLRNW-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1P7IC50 :  1000000   nM  PDBBind
1P7IC50:  1000000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.609α = 90
b = 74.609β = 90
c = 49.897γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary