1G49

A CARBOXYLIC ACID BASED INHIBITOR IN COMPLEX WITH MMP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Development of new hydroxamate matrix metalloproteinase inhibitors derived from functionalized 4-aminoprolines.

Natchus, M.G.Bookland, R.G.De, B.Almstead, N.G.Pikul, S.

(2000) J Med Chem 43: 4948-4963

  • DOI: 10.1021/jm000246e
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of hydroxamates was prepared from an aminoproline scaffold and tested for efficacy as matrix metalloproteinase (MMP) inhibitors. Detailed SAR for the series is reported for five enzymes within the MMP family, and a number of inhibitors, such ...

    A series of hydroxamates was prepared from an aminoproline scaffold and tested for efficacy as matrix metalloproteinase (MMP) inhibitors. Detailed SAR for the series is reported for five enzymes within the MMP family, and a number of inhibitors, such as compound 47, display broad-spectrum activity with sub-nanomolar potency for some enzymes. Modifications of the P1' portion of the molecule played a key role in affecting both potency and selectivity within the MMP family. Longer-chain aliphatic substituents in this region of the molecule tended to increase potency for MMP-3 and decrease potency for MMP-1, as exemplified by compounds 48-50, while aromatic substituents, as in compound 52, generated broad-spectrum inhibition. The data is rationalized based upon X-ray crystal data which is also presented. While the in vitro peroral absorption seemed to be less predictable, it tended to decrease with longer and more hydrophilic substituents. Finally, a rat model of osteoarthritis was used to evaluate the efficacy of these compounds, and a direct link was established between their pharmacokinetics and their in vivo efficacy.


    Organizational Affiliation

    Procter and Gamble Pharmaceuticals, 8700 Mason-Montgomery Road, Mason, Ohio 45040, USA. natchus.mg@pg.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MATRIX METALLOPROTEINASE 3
A, B
173Homo sapiensMutation(s): 0 
Gene Names: MMP3STMY1
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS  P08254
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
111
Query on 111

Download CCD File 
B
(1N)-4-N-BUTOXYPHENYLSULFONYL-(2R)-N-HYDROXYCARBOXAMIDO-(4S)-METHANESULFONYLAMINO-PYRROLIDINE
C16 H25 N3 O7 S2
ULDXUWXTVRRUND-SWLSCSKDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
111IC50:  16   nM  Binding MOAD
111IC50 :  16   nM  PDBBind
111IC50:  16   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.668α = 90
b = 77.112β = 90
c = 106.145γ = 90
Software Package:
Software NamePurpose
FFTmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description