Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-hydroxy-2-(4-methoxy-N(2-(3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)ethyl)phenylsulfonamido)acetamide

Experimental Data Snapshot

  • Resolution: 1.81 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs).

Attolino, E.Calderone, V.Dragoni, E.Fragai, M.Richichi, B.Luchinat, C.Nativi, C.

(2010) Eur J Med Chem 45: 5919-5925

  • DOI: https://doi.org/10.1016/j.ejmech.2010.09.057
  • Primary Citation of Related Structures:  
    3N2U, 3N2V

  • PubMed Abstract: 

    N-arylsulfonyl-based MMPs inhibitors (MMPIs) are among the most prominent inhibitors possessing nanomolar affinity. However, their poor bioavailability remains critical for the drug development of this family of molecules. The structural analysis of the complex of NNGH (the most representative member of the family) with MMP-12 provided us with the basis to effectively design simple NNGH analogues with enhanced solubility in water. Following this approach, the sec-butyl residue, not directly involved in the binding with MMP, has been replaced with hydrophilic residues thus yielding new potent inhibitors soluble in water.

  • Organizational Affiliation

    ProtEra s.r.l. viale delle Idee, 22 I-50019 Sesto F.no (FI), Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage metalloelastase158Homo sapiensMutation(s): 1 
Gene Names: MMP12HME
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
GTEx:  ENSG00000262406 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39900
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
D3X BindingDB:  3N2U Ki: min: 14, max: 14.3 (nM) from 2 assay(s)
PDBBind:  3N2U Ki: 14.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.81 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.394α = 90
b = 60.446β = 114.67
c = 54.043γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description