3ELM

Crystal Structure of MMP-13 Complexed with Inhibitor 24f


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jm801394m
  • Primary Citation of Related Structures:  
    3ELM

  • 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.


Macromolecules
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
PHAROS:  P45452
GTEx:  ENSG00000137745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
24F
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
GYETWAWIKBOMPE-OAQYLSRUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [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]
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]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
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)
Binding MOAD:  3ELM Ki: 0.19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
PDB_EXTRACTdata extraction
CNXrefinement

Structure Validation

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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