3ELM

Crystal Structure of MMP-13 Complexed with Inhibitor 24f


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of potent, selective, and orally active carboxylic acid based inhibitors of matrix metalloproteinase-13

Monovich, L.G.Tommasi, R.A.Fujimoto, R.A.Blancuzzi, V.Clark, K.Cornell, W.D.Doti, R.Doughty, J.Fang, J.Farley, D.Fitt, J.Ganu, V.Goldberg, R.Goldstein, R.Lavoie, S.Kulathila, R.Macchia, W.Parker, D.T.Melton, R.O'Byrne, E.Pastor, G.Pellas, T.Quadros, E.Reel, N.Roland, D.M.Sakane, Y.Singh, H.Skiles, J.Somers, J.Toscano, K.Wigg, A.Zhou, S.Zhu, L.Shieh, W.C.Xue, S.McQuire, L.W.

(2009) J.Med.Chem. 52: 3523-3538

  • DOI: 10.1021/jm801394m

  • PubMed Abstract: 
  • The matrix metalloproteinase enzyme MMP-13 plays a key role in the degradation of type II collagen in cartilage and bone in osteoarthritis (OA). An effective MMP-13 inhibitor would therefore be a novel disease modifying therapy for the treatment of a ...

    The matrix metalloproteinase enzyme MMP-13 plays a key role in the degradation of type II collagen in cartilage and bone in osteoarthritis (OA). An effective MMP-13 inhibitor would therefore be a novel disease modifying therapy for the treatment of arthritis. Our efforts have resulted in the discovery of a series of carboxylic acid inhibitors of MMP-13 that do not significantly inhibit the related MMP-1 (collagenase-1) or tumor necrosis factor-alpha (TNF-alpha) converting enzyme (TACE). It has previously been suggested (but not proven) that inhibition of the latter two enzymes could lead to side effects. A promising carboxylic acid lead 9 was identified and a convergent synthesis developed. This paper describes the optimization of 9 and the identification of a compound 24f for further development. Compound 24f is a subnanomolar inhibitor of MMP-13 (IC(50) value 0.5 nM and K(i) of 0.19 nM) having no activity against MMP-1 or TACE (IC(50) of >10000 nM). Furthermore, in a rat model of MMP-13-induced cartilage degradation, 24f significantly reduced proteoglycan release following oral dosing at 30 mg/kg (75% inhibition, p < 0.05) and at 10 mg/kg (40% inhibition, p < 0.05).


    Organizational Affiliation

    Arthritis and Bone Metabolism Research, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
171Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
24F
Query on 24F

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Download CCD File 
A, B
(2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1-[(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid
C23 H30 N2 O7 S2
GYETWAWIKBOMPE-OAQYLSRUSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24FIC50: 0.5 nM (100) BINDINGDB
24FKi: 0.2 nM (100) BINDINGDB
24FIC50: 0.5 nM BINDINGMOAD
24FKi: 0.19 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.500α = 90.00
b = 36.070β = 130.53
c = 95.180γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description