2HVX

Discovery of Potent, Orally Active, Nonpeptide Inhibitors of Human Mast Cell Chymase by Using Structure-Based Drug Design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of potent, selective, orally active, nonpeptide inhibitors of human mast cell chymase.

Greco, M.N.Hawkins, M.J.Powell, E.T.Almond, H.R.de Garavilla, L.Hall, J.Minor, L.K.Wang, Y.Corcoran, T.W.Di Cera, E.Cantwell, A.M.Savvides, S.N.Damiano, B.P.Maryanoff, B.E.

(2007) J Med Chem 50: 1727-1730

  • DOI: https://doi.org/10.1021/jm0700619
  • Primary Citation of Related Structures:  
    2HVX

  • PubMed Abstract: 

    A series of beta-carboxamido-phosphon(in)ic acids (2) was identified as a new structural motif for obtaining potent inhibitors of human mast cell chymase. For example, 1-naphthyl derivative 5f had an IC50 value of 29 nM and (E)-styryl derivative 6g had an IC50 value of 3.5 nM. An X-ray structure for 5f.chymase revealed key interactions within the enzyme active site. Compound 5f was selective for inhibiting chymase versus eight serine proteases. Compound 6h was orally bioavailable in rats (F=39%), and orally efficacious in a hamster model of inflammation.


  • Organizational Affiliation

    Research and Early Development, Johnson & Johnson Pharmaceutical Research and Development, Spring House, Pennsylvania 19477-0776, USA. mgreco@prdus.jnj.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chymase226Homo sapiensMutation(s): 3 
EC: 3.4.21.39
UniProt & NIH Common Fund Data Resources
Find proteins for P23946 (Homo sapiens)
Explore P23946 
Go to UniProtKB:  P23946
PHAROS:  P23946
GTEx:  ENSG00000092009 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23946
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DRX
Query on DRX

Download Ideal Coordinates CCD File 
B [auth A][(1S)-1-(5-CHLORO-1-BENZOTHIEN-3-YL)-2-(2-NAPHTHYLAMINO)-2-OXOETHYL]PHOSPHONIC ACID
C20 H15 Cl N O4 P S
HUJXISJLAPAFBO-IBGZPJMESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DRX BindingDB:  2HVX Ki: 36 (nM) from 1 assay(s)
IC50: 29 (nM) from 1 assay(s)
PDBBind:  2HVX IC50: 29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.245 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.94α = 90
b = 73.94β = 90
c = 49.45γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.4: 2021-10-20
    Changes: Advisory, Database references, Derived calculations