3KEK

Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.

Schnute, M.E.O'Brien, P.M.Nahra, J.Morris, M.Howard Roark, W.Hanau, C.E.Ruminski, P.G.Scholten, J.A.Fletcher, T.R.Hamper, B.C.Carroll, J.N.Patt, W.C.Shieh, H.S.Collins, B.Pavlovsky, A.G.Palmquist, K.E.Aston, K.W.Hitchcock, J.Rogers, M.D.McDonald, J.Johnson, A.R.Munie, G.E.Wittwer, A.J.Man, C.F.Settle, S.L.Nemirovskiy, O.Vickery, L.E.Agawal, A.Dyer, R.D.Sunyer, T.

(2009) Bioorg Med Chem Lett 20: 576-580

  • DOI: 10.1016/j.bmcl.2009.11.081
  • Primary Citation of Related Structures:  
    3KEJ, 3KEK, 3KEC

  • PubMed Abstract: 
  • Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not ligands for the catalytic zinc atom ...

    Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not ligands for the catalytic zinc atom. Compound 29b demonstrated reduction of cartilage degradation biomarker (TIINE) levels associated with cartilage protection in a preclinical rat osteoarthritis model.


    Organizational Affiliation

    Global Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, St. Louis, MO 63017, USA. mark.e.schnute@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagenase 3 AB167Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
NIH Common Fund Data Resources
PHAROS:  P45452
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3EKKi:  4.400000095367432   nM  Binding MOAD
3EKKi :  4.400000095367432   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.846α = 90
b = 95.74β = 90
c = 36.443γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description