1HY7

A CARBOXYLIC ACID BASED INHIBITOR IN COMPLEX WITH MMP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Development of new carboxylic acid-based MMP inhibitors derived from functionalized propargylglycines.

Natchus, M.G.Bookland, R.G.Laufersweiler, M.J.Pikul, S.Almstead, N.G.De, B.Janusz, M.J.Hsieh, L.C.Gu, F.Pokross, M.E.Patel, V.S.Garver, S.M.Peng, S.X.Branch, T.M.King, S.L.Baker, T.R.Foltz, D.J.Mieling, G.E.

(2001) J Med Chem 44: 1060-1071

  • DOI: 10.1021/jm000477l
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of carboxylic acids were prepared from a propargylglycine scaffold and tested for efficacy as matrix metalloproteinase (MMP) inhibitors. Detailed SAR for the series is reported for four enzymes within the MMP family. The inhibitors were typically potent against collagenase-3 (MMP-13) and gelatinase A (MMP-2), while they spared collagenase-1 (MMP-1) and only moderately inhibited stromelysin (MMP-3) ...

    A series of carboxylic acids were prepared from a propargylglycine scaffold and tested for efficacy as matrix metalloproteinase (MMP) inhibitors. Detailed SAR for the series is reported for four enzymes within the MMP family. The inhibitors were typically potent against collagenase-3 (MMP-13) and gelatinase A (MMP-2), while they spared collagenase-1 (MMP-1) and only moderately inhibited stromelysin (MMP-3). Compound 40 represents a typical inhibition profile of a compound with reasonable potency. Introduction of polar groups was required in order to generate inhibitors with acceptable water solubility, and this often resulted in a loss of potency as in compound 63. High serum protein binding proved to be a difficult hurdle with many compounds such as 48 showing >99% binding. Some compounds such as 64 displayed approximately 90% binding, but no reliable method was discovered for designing molecules with low protein binding. Finally, selected data regarding the pharmacokinetic behavior of these compounds is presented.


    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
STROMELYSIN-1A, B173Homo sapiensMutation(s): 0 
Gene Names: MMP3STMY1
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
NIH Common Fund Data Resources
PHAROS  P08254
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
MBS
Query on MBS

Download CCD File 
B
R-2-{[4'-METHOXY-(1,1'-BIPHENYL)-4-YL]-SULFONYL}-AMINO-6-METHOXY-HEX-4-YNOIC ACID
C20 H21 N O6 S
QJKGJGURDPRKGW-LJQANCHMSA-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 %)
MBSIC50 :  4090.000244140625   nM  PDBBind
MBSIC50:  4090   nM  Binding MOAD
MBSIC50:  4090   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.918α = 90
b = 78.059β = 90
c = 105.801γ = 90
Software Package:
Software NamePurpose
FFTmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2002-01-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-02-07
    Changes: Experimental preparation