PDBsum entry 1ztq

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
162 a.a. *
153 a.a. *
033 ×4
_ZN ×8
_CA ×12
Waters ×502
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the catalytic domain of mmp-13 complexed with way-033
Structure: Collagenase 3. Chain: a, b, c, d. Fragment: mmp-13 catalytic domain. Synonym: matrix metalloproteinase-13, mmp-13. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: mmp13. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.236     R-free:   0.287
Authors: J.Wu,T.S.Rush Iii,R.Hotchandani,X.Du,M.Geck,E.Collins, Z.B.Xu,J.Skotnicki,J.I.Levin,F.Lovering
Key ref: J.Wu et al. (2005). Identification of potent and selective MMP-13 inhibitors. Bioorg Med Chem Lett, 15, 4105-4109. PubMed id: 16005220 DOI: 10.1016/j.bmcl.2005.06.019
27-May-05     Release date:   30-May-06    
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Protein chains
Pfam   ArchSchema ?
P45452  (MMP13_HUMAN) -  Collagenase 3
471 a.a.
162 a.a.
Protein chains
Pfam   ArchSchema ?
P45452  (MMP13_HUMAN) -  Collagenase 3
471 a.a.
153 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     collagen catabolic process   2 terms 
  Biochemical function     metallopeptidase activity     3 terms  


DOI no: 10.1016/j.bmcl.2005.06.019 Bioorg Med Chem Lett 15:4105-4109 (2005)
PubMed id: 16005220  
Identification of potent and selective MMP-13 inhibitors.
J.Wu, T.S.Rush, R.Hotchandani, X.Du, M.Geck, E.Collins, Z.B.Xu, J.Skotnicki, J.I.Levin, F.E.Lovering.
A potent, selective series of MMP-13 inhibitors has been derived from a weak (3.2 microM) inhibitor that did not bear a zinc chelator. Structure-based drug design strategies were employed to append a Zn-chelating group to one end of the molecule and functionality to enhance selectivity to the other. A compound from this series demonstrated rat oral bioavailability and efficacy in a bovine articular cartilage explant model.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21507637 T.E.Barta, D.P.Becker, L.J.Bedell, A.M.Easton, S.L.Hockerman, J.Kiefer, G.E.Munie, K.J.Mathis, M.H.Li, J.G.Rico, C.I.Villamil, and J.M.Williams (2011).
MMP-13 selective α-sulfone hydroxamates: a survey of P1' heterocyclic amide isosteres.
  Bioorg Med Chem Lett, 21, 2820-2822.  
21493063 Y.M.Fobian, J.N.Freskos, T.E.Barta, L.J.Bedell, R.Heintz, D.J.Kassab, J.R.Kiefer, B.V.Mischke, J.M.Molyneaux, P.Mullins, G.E.Munie, and D.P.Becker (2011).
MMP-13 selective alpha-sulfone hydroxamates: identification of selective P1' amides.
  Bioorg Med Chem Lett, 21, 2823-2825.  
20824169 R.Kothapalli, A.M.Khan, Basappa, A.Gopalsamy, Y.S.Chong, and L.Annamalai (2010).
Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domain.
  PLoS One, 5, e12494.  
20486866 Y.Itoh (2010).
Metalloproteinase binding proteins: WO2009097397.
  Expert Opin Ther Pat, 20, 1091-1095.  
17084612 D.A.Erlanson (2006).
Fragment-based lead discovery: a chemical update.
  Curr Opin Biotechnol, 17, 643-652.  
16569256 J.P.Pelletier, J.Martel-Pelletier, and J.P.Raynauld (2006).
Most recent developments in strategies to reduce the progression of structural changes in osteoarthritis: today and tomorrow.
  Arthritis Res Ther, 8, 206.  
16216515 Y.Hu, J.S.Xiang, M.J.DiGrandi, X.Du, M.Ipek, L.M.Laakso, J.Li, W.Li, T.S.Rush, J.Schmid, J.S.Skotnicki, S.Tam, J.R.Thomason, Q.Wang, and J.I.Levin (2005).
Potent, selective, and orally bioavailable matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.
  Bioorg Med Chem, 13, 6629-6644.  
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