2OW9

Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects.

Johnson, A.R., Pavlovsky, A.G., Ortwine, D.F., Prior, F., Man, C.F., Bornemeier, D.A., Banotai, C.A., Mueller, W.T., McConnell, P., Yan, C., Baragi, V., Lesch, C., Roark, W.H., Wilson, M., Datta, K., Guzman, R., Han, H.K., Dyer, R.D.

(2007) J.Biol.Chem. 282: 27781-27791

  • DOI: 10.1074/jbc.M703286200
  • Primary Citation of Related Structures:  
  • Also Cited By: 3DPF, 3DPE, 3DNG

  • PubMed Abstract: 

    • Matrix metalloproteinase-13 (MMP13) is a Zn(2+)-dependent protease that catalyzes the cleavage of type II collagen, the main structural protein in articular cartilage. Excess MMP13 activity causes cartilage degradation in osteoarthritis, making this ...

    Matrix metalloproteinase-13 (MMP13) is a Zn(2+)-dependent protease that catalyzes the cleavage of type II collagen, the main structural protein in articular cartilage. Excess MMP13 activity causes cartilage degradation in osteoarthritis, making this protease an attractive therapeutic target. However, clinically tested MMP inhibitors have been associated with a painful, joint-stiffening musculoskeletal side effect that may be due to their lack of selectivity. In our efforts to develop a disease-modifying osteoarthritis drug, we have discovered MMP13 inhibitors that differ greatly from previous MMP inhibitors; they do not bind to the catalytic zinc ion, they are noncompetitive with respect to substrate binding, and they show extreme selectivity for inhibiting MMP13. By structure-based drug design, we generated an orally active MMP13 inhibitor that effectively reduces cartilage damage in vivo and does not induce joint fibroplasias in a rat model of musculoskeletal syndrome side effects. Thus, highly selective inhibition of MMP13 in patients may overcome the major safety and efficacy challenges that have limited previously tested non-selective MMP inhibitors. MMP13 inhibitors such as the ones described here will help further define the role of this protease in arthritis and other diseases and may soon lead to drugs that safely halt cartilage damage in patients.

    Organizational Affiliation: 

    Department of Inflammation Molecular Sciences, Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA. adam.johnson@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
170Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAE
Query on HAE
Download SDF File 
Download CCD File 
A, B
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SP6
Query on SP6
Download SDF File 
Download CCD File 
A, B
BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE
C21 H16 N2 O4 S
PLBINCOCFGQAJM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SP6IC50: 23 - 51 nM (98) BINDINGDB
SP6Ki: 64 nM (98) BINDINGDB
SP6IC50: 30 nM BINDINGMOAD
SP6IC50: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 140.764α = 90.00
b = 36.343β = 93.53
c = 71.684γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-02-15 
  • Released Date: 2007-02-27 
  • Deposition Author(s): Pavlovsky, A.G.

Revision History 

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2007-09-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description