Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

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Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation.

Scannevin, R.H.Alexander, R.Haarlander, T.M.Burke, S.L.Singer, M.Huo, C.Zhang, Y.M.Maguire, D.Spurlino, J.Deckman, I.Carroll, K.I.Lewandowski, F.Devine, E.Dzordzorme, K.Tounge, B.Milligan, C.Bayoumy, S.Williams, R.Schalk-Hihi, C.Leonard, K.Jackson, P.Todd, M.Kuo, L.C.Rhodes, K.J.

(2017) J Biol Chem 292: 17963-17974

  • DOI: https://doi.org/10.1074/jbc.M117.806075
  • Primary Citation of Related Structures:  
    5UE3, 5UE4

  • PubMed Abstract: 

    Aberrant activation of matrix metalloproteinases (MMPs) is a common feature of pathological cascades observed in diverse disorders, such as cancer, fibrosis, immune dysregulation, and neurodegenerative diseases. MMP-9, in particular, is highly dynamically regulated in several pathological processes. Development of MMP inhibitors has therefore been an attractive strategy for therapeutic intervention. However, a long history of failed clinical trials has demonstrated that broad-spectrum MMP inhibitors have limited clinical utility, which has spurred the development of inhibitors selective for individual MMPs. Attaining selectivity has been technically challenging because of sequence and structural conservation across the various MMPs. Here, through a biochemical and structural screening paradigm, we have identified JNJ0966, a highly selective compound that inhibited activation of MMP-9 zymogen and subsequent generation of catalytically active enzyme. JNJ0966 had no effect on MMP-1, MMP-2, MMP-3, MMP-9, or MMP-14 catalytic activity and did not inhibit activation of the highly related MMP-2 zymogen. The molecular basis for this activity was characterized as an interaction of JNJ0966 with a structural pocket in proximity to the MMP-9 zymogen cleavage site near Arg-106, which is distinct from the catalytic domain. JNJ0966 was efficacious in reducing disease severity in a mouse experimental autoimmune encephalomyelitis model, demonstrating the viability of this therapeutic approach. This discovery reveals an unprecedented pharmacological approach to MMP inhibition, providing an opportunity to improve selectivity of future clinical drug candidates. Targeting zymogen activation in this manner may also allow for pharmaceutical exploration of other enzymes previously viewed as intractable drug targets.

  • Organizational Affiliation

    From Janssen Research and Development, LLC, Spring House, Pennsylvania 19477 rscannevin@yumanity.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9
A, B
236Homo sapiensMutation(s): 0 
Gene Names: MMP9CLG4B
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
PHAROS:  P14780
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
C4 H12 N O3
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
N [auth B]
O [auth B]
P [auth B]
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.3α = 90
b = 73.2β = 106.3
c = 77.5γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Advisory, Data collection, Database references, Derived calculations