5I4O

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors.

Nuti, E., Cuffaro, D., D'Andrea, F., Rosalia, L., Tepshi, L., Fabbi, M., Carbotti, G., Ferrini, S., Santamaria, S., Camodeca, C., Ciccone, L., Orlandini, E., Nencetti, S., Stura, E.A., Dive, V., Rossello, A.

(2016) Chemmedchem 11: 1626-1637

  • DOI: 10.1002/cmdc.201600235
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Matrix metalloproteinase-12 (MMP-12) can be considered an attractive target to study selective inhibitors useful in the development of new therapies for lung and cardiovascular diseases. In this study, a new series of arylsulfonamide carboxylates, wi ...

    Matrix metalloproteinase-12 (MMP-12) can be considered an attractive target to study selective inhibitors useful in the development of new therapies for lung and cardiovascular diseases. In this study, a new series of arylsulfonamide carboxylates, with increased hydrophilicity resulting from conjugation with a β-N-acetyl-d-glucosamine moiety, were designed and synthesized as MMP-12 selective inhibitors. Their inhibitory activity was evaluated on human MMPs by using the fluorimetric assay, and a crystallographic analysis was performed to characterize their binding mode. Among these glycoconjugates, a nanomolar MMP-12 inhibitor with improved water solubility, compound 3 [(R)-2-(N-(2-(3-(2-acetamido-2-deoxy-β-d-glucopyranosyl)thioureido)ethyl)biphenyl-4-ylsulfonamido)-3-methylbutanoic acid], was identified.

    Organizational Affiliation: 

    Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A, B, C, D
159Homo sapiensMutation(s): 0 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V28
Query on V28
Download SDF File 
Download CCD File 
A, B, C, D
N-({1-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1H-1,2,3-triazol-4-yl}methyl)-N-[([1,1'-biphenyl]-4-yl)sulfonyl]-D-valine
C28 H35 N5 O9 S
KNBZJXWGCBPDHT-ZRRJEQDASA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.980α = 90.00
b = 63.510β = 102.31
c = 78.640γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Source and taxonomy