2OW9 | pdb_00002ow9

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 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2OW9

Ligand Structure Quality Assessment 


This is version 1.4 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 Biological Chem 282: 27781-27791

  • DOI: https://doi.org/10.1074/jbc.M703286200
  • Primary Citation Related Structures: 
    2OW9, 2OZR

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 39.71 kDa 
  • Atom Count: 3,195 
  • Modeled Residue Count: 333 
  • Deposited Residue Count: 340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagenase 3
A, B
170Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
PHAROS:  P45452
GTEx:  ENSG00000137745 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SP6

Query on SP6



Download:Ideal Coordinates CCD File
I [auth A],
Q [auth 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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
HAE

Query on HAE



Download:Ideal Coordinates CCD File
J [auth A],
R [auth B]
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
K [auth B],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
M [auth B]
N [auth B]
E [auth A],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SP6 BindingDB:  2OW9 Ki: 64 (nM) from 1 assay(s)
IC50: min: 23, max: 51 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.764α = 90
b = 36.343β = 93.53
c = 71.684γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2007-09-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description