Solution structure of matrix metalloproteinase 3 (MMP-3) in the presence of 3-4'-cyanobyphenyl-4-yloxy)-n-hdydroxypropionamide (MMP-3 inhibitor VII)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

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Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors

Alcaraz, L.A.Banci, L.Bertini, I.Cantini, F.Donaire, A.Gonnelli, L.

(2007) J Biol Inorg Chem 12: 1197-1206

  • DOI: https://doi.org/10.1007/s00775-007-0288-9
  • Primary Citation of Related Structures:  
    2JNP, 2JT5, 2JT6

  • PubMed Abstract: 

    We structurally characterized the adducts of the catalytic domain of matrix metalloproteinase-3 (MMP3) with three different nonpeptidic inhibitors by solving the solution structure of one adduct [MMP3-N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid] and then by calculating structural models of the other two adducts using a reduced set of experimental NMR data, following a recently proposed procedure (Bertini et al. in J. Med. Chem. 48:7544-7559, 2005). The inhibitors were selected with the criteria of maintaining in all of them the same zinc-coordinating moiety and of selectively changing the substituents and/or the functional groups. The backbone dynamics on various time scales have been characterized as well. The comparison among these structures and with others previously reported allowed us to elucidate fine details of inhibitor-receptor interactions and to develop some criteria, which could guide in optimizing the design of selective inhibitors.

  • Organizational Affiliation

    Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stromelysin-1161Homo sapiensMutation(s): 0 
Gene Names: MMP3STMY1
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens)
Explore P08254 
Go to UniProtKB:  P08254
PHAROS:  P08254
GTEx:  ENSG00000149968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08254
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
JT6 PDBBind:  2JT6 Ki: 25 (nM) from 1 assay(s)
BindingDB:  2JT6 Kd: min: 100, max: 110 (nM) from 2 assay(s)
IC50: min: 25, max: 57 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-02-19
    Changes: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Other
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations