Solution structure of matrix metalloproteinase 3 (MMP-3) in the presence of N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 25 
  • Selection Criteria: target function 

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This is version 1.4 of the entry. See complete history


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
Matrix metalloproteinase-3161Homo 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
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NGH

Download Ideal Coordinates CCD File 
C13 H20 N2 O5 S
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
NGH BindingDB:  2JNP Ki: min: 132, max: 133 (nM) from 2 assay(s)
IC50: 6500 (nM) from 1 assay(s)
PDBBind:  2JNP Ki: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 25 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-05-08
    Changes: Database references