1ROS

Crystal structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl-4-(4-ethoxy[1,1-biphenyl]-4-yl)-4-oxobutanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12.

Morales, R.Perrier, S.Florent, J.M.Beltra, J.Dufour, S.De Mendez, I.Manceau, P.Tertre, A.Moreau, F.Compere, D.Dublanchet, A.C.O'Gara, M.

(2004) J Mol Biol 341: 1063-1076

  • DOI: 10.1016/j.jmb.2004.06.039
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human macrophage elastase (MMP-12) plays an important role in inflammatory processes and has been implicated in diseases such as emphysema and chronic obstructive pulmonary disease (COPD). It is therefore an attractive target for therapeutic agents. ...

    Human macrophage elastase (MMP-12) plays an important role in inflammatory processes and has been implicated in diseases such as emphysema and chronic obstructive pulmonary disease (COPD). It is therefore an attractive target for therapeutic agents. As part of a structure-based drug design programme to find new inhibitors of MMP-12, the crystal structures of the MMP-12 catalytic domain (residues 106-268) complexed to three different non-peptidic small molecule inhibitors have been determined. The structures reveal that all three ligands bind in the S1' pocket but show varying degrees of interaction with the Zn atom. The structures of the complexes with inhibitors CP-271485 and PF-00356231 reveal that their central morpholinone and thiophene rings, respectively, sit over the Zn atom at a distance of approximately 5A, locating the inhibitors halfway down the S1' pocket. In both of these structures, an acetohydroxamate anion, an artefact of the crystallisation solution, chelates the zinc atom. By contrast, the acetohydroxamate anion is displaced by the ligand in the structure of MMP-12 complexed to PD-0359601 (Bayer), a potent zinc chelating N-substituted biaryl butyric acid, used as a reference compound for crystallisation. Although a racemate was used for the crystallisation, the S enantiomer only is bound in the crystal. Important hydrophobic interactions between the inhibitors and residues from the S1' pocket are observed in all of the structures. The relative selectivity displayed by these ligands for MMP-12 over other MMP family members is discussed.


    Organizational Affiliation

    Pfizer Global Research and Development, Fresnes Laboratories, 94265 Fresnes Cedex, France [corrected]



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastaseA, B163Homo sapiensMutation(s): 0 
Gene Names: MMP12HME
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
NIH Common Fund Data Resources
PHAROS  P39900
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEO
Query on DEO

Download CCD File 
A, B
2-[2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)ETHYL]-4-(4'-ETHOXY-1,1'-BIPHENYL-4-YL)-4-OXOBUTANOIC ACID
C28 H25 N O6
AQYSXARQCHHHLK-NRFANRHFSA-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 %)
DEOIC50 :  1.7000000476837158   nM  PDBBind
DEOIC50:  1.7000000476837158   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.2α = 90
b = 123.2β = 90
c = 59.5γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description