1YOU

Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent pyrimidinetrione-based inhibitors of MMP-13 with enhanced selectivity over MMP-14.

Blagg, J.A.Noe, M.C.Wolf-Gouveia, L.A.Reiter, L.A.Laird, E.R.Chang, S.P.Danley, D.E.Downs, J.T.Elliott, N.C.Eskra, J.D.Griffiths, R.J.Hardink, J.R.Haugeto, A.I.Jones, C.S.Liras, J.L.Lopresti-Morrow, L.L.Mitchell, P.G.Pandit, J.Robinson, R.P.Subramanyam, C.Vaughn-Bowser, M.L.Yocum, S.A.

(2005) Bioorg.Med.Chem.Lett. 15: 1807-1810

  • DOI: 10.1016/j.bmcl.2005.02.038

  • PubMed Abstract: 
  • Through the use of computational modeling, a series of pyrimidinetrione-based inhibitors of MMP-13 was designed based on a lead inhibitor identified through file screening. Incorporation of a biaryl ether moiety at the C-5 position of the pyrimidinet ...

    Through the use of computational modeling, a series of pyrimidinetrione-based inhibitors of MMP-13 was designed based on a lead inhibitor identified through file screening. Incorporation of a biaryl ether moiety at the C-5 position of the pyrimidinetrione ring resulted in a dramatic enhancement of MMP-13 potency. Protein crystallography revealed that this moiety binds in the S(1)(') pocket of the enzyme. Optimization of the C-4 substituent of the terminal aromatic ring led to incorporation of selectivity versus MMP-14 (MT-1 MMP). Structure activity relationships of the biaryl ether substituent are presented as is pharmacokinetic data for a compound that meets our in vitro potency and selectivity goals.


    Organizational Affiliation

    Pfizer Global Research and Development, Groton Laboratories, MS8220-2471, Eastern Point Road, Groton, CT 06340, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
168Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens)
Go to Gene View: MMP13
Go to UniProtKB:  P45452
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PFD
Query on PFD

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Download CCD File 
A, B
5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
C20 H19 F N2 O6
XRSYNYGEEYTXJV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PFDIC50: 0.6 nM (100) BINDINGDB
PFDIC50: 0.87 nM BINDINGMOAD
PFDIC50: 0.87 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.089α = 90.00
b = 108.223β = 90.00
c = 36.035γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-01-28 
  • Released Date: 2005-03-15 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance