Crystal Structure of MMP-13 Complexed with Inhibitor 24f

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm801394m
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagenase 3
A, B
171Homo 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
GTEx:  ENSG00000137745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 24F

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]
(2R)-({[5-(4-ethoxyphenyl)thiophen-2-yl]sulfonyl}amino){1-[(1-methylethoxy)carbonyl]piperidin-4-yl}ethanoic acid
C23 H30 N2 O7 S2
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]
H [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
24F PDBBind:  3ELM Ki: 0.19 (nM) from 1 assay(s)
BindingDB:  3ELM Ki: 0.19 (nM) from 1 assay(s)
IC50: 0.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.5α = 90
b = 36.07β = 130.53
c = 95.18γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations