5H8X

Crystal structure of the complex MMP-8/BF471 (catechol inhibitor)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catechol-based matrix metalloproteinase inhibitors with additional antioxidative activity.

Tauro, M.Laghezza, A.Loiodice, F.Piemontese, L.Caradonna, A.Capelli, D.Montanari, R.Pochetti, G.Di Pizio, A.Agamennone, M.Campestre, C.Tortorella, P.

(2016) J Enzyme Inhib Med Chem 31: 25-37

  • DOI: 10.1080/14756366.2016.1217853

  • PubMed Abstract: 
  • New catechol-containing chemical entities have been investigated as matrix metalloproteinase inhibitors as well as antioxidant molecules. The combination of the two properties could represent a useful feature due to the potential application in all t ...

    New catechol-containing chemical entities have been investigated as matrix metalloproteinase inhibitors as well as antioxidant molecules. The combination of the two properties could represent a useful feature due to the potential application in all the pathological processes characterized by increased proteolytic activity and radical oxygen species (ROS) production, such as inflammation and photoaging. A series of catechol-based molecules were synthesized and tested for both proteolytic and oxidative inhibitory activity, and the detailed binding mode was assessed by crystal structure determination of the complex between a catechol derivative and the matrix metalloproteinase-8. Surprisingly, X-ray structure reveals that the catechol oxygens do not coordinates the zinc atom.


    Organizational Affiliation

    a Department of Tumor Biology , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil collagenase
A
163Homo sapiensMutation(s): 0 
Gene Names: MMP8 (CLG1)
EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens)
Go to Gene View: MMP8
Go to UniProtKB:  P22894
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7FY
Query on 7FY

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Download CCD File 
A
~{N}-[4,5-bis(oxidanylidene)cyclohexen-1-yl]-4-phenyl-benzenesulfonamide
C18 H15 N O4 S
APAOLMVDZOWNQC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
5XT
Query on 5XT

Download SDF File 
Download CCD File 
A
~{N}-[3,4-bis(oxidanyl)phenyl]-4-phenyl-benzenesulfonamide
C18 H15 N O4 S
OGGBNPCRZSBOOJ-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.910α = 90.00
b = 68.460β = 90.00
c = 68.530γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references