3DNG

Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S(1)' Subsite of Matrix Metalloproteinase 8 (MMP-8)

Pochetti, G.Montanari, R.Gege, C.Chevrier, C.Taveras, A.G.Mazza, F.

(2009) J.Med.Chem. 52: 1040-1049

  • DOI: 10.1021/jm801166j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mode of binding and the activity of the first two non-zinc chelating, potent, and selective inhibitors of human neutrophil collagenase are reported. The crystal structures of the catalytic domain of MMP-8, respectively complexed with each inhibit ...

    The mode of binding and the activity of the first two non-zinc chelating, potent, and selective inhibitors of human neutrophil collagenase are reported. The crystal structures of the catalytic domain of MMP-8, respectively complexed with each inhibitor, reveals that both ligands are deeply inserted into the primary specificity subsite S(1)', where they induce a similar conformational change of the surrounding loop that is endowed with the main specificity determinants of MMPs. Accord to this rearrangement, both inhibitors remove the floor of the pocket formed by the Y227 side-chain, rendering available an extra binding region never explored before. The present data show that potent and more selective inhibitors can be obtained by developing ligands able to interact with the selectivity regions of the enzyme rather than with the catalytic zinc ion, which is the common feature of all MMP members.


    Related Citations: 
    • Structural basis for the highly selective inhibition of MMP-13
      Engel, C.K.,Pirard, B.,Schimanski, S.,Kirsch, R.,Habermann, J.,Klingler, O.,Schlotte, V.,Weithmann, K.U.,Wendt, K.U.
      (2005) Chem.Biol. 12: 181
    • Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12
      Morales, R.,Perrier, S.,Florent, J.M.,Beltra, J.,Dufour, S.,De Mendez, I.,Manceau, P.,Tertre, A.,Moreau, F.,Compere, D.,Dublanchet, A.C.,O'Gara, M.
      (2004) J.Mol.Biol. 341: 1063
    • Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects
      Johnson, A.R.,Pavlovsky, A.G.,Ortwine, D.F.,Prior, F.,Man, C.F.,Bornemeier, D.A.,Banotai, C.A.,Mueller, W.T.,McConnell, P.,Yan, C.,Baragi, V.,Lesch, C.,Roark, W.H.,Wilson, M.,Datta, K.,Guzman, R.,Han, H.K.,Dyer, R.D.
      (2007) J.Biol.Chem. 282: 27781


    Organizational Affiliation

    Istituto di Cristallografia-CNR, Area della Ricerca Roma 1, Via Salaria Km.29,300, I-00016 Monterotondo Stazione, Roma, Italy. giorgio.pochetti@ic.cnr.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil collagenase
A, B
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AXA
Query on AXA

Download SDF File 
Download CCD File 
A, B
(5S)-5-(2-amino-2-oxoethyl)-4-oxo-N-[(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-6-yl)methyl]-3,4,5,6,7,8-hexahydro[1]benzothieno[2,3-d]pyrimidine-2-carboxamide
C22 H21 N5 O5 S
ITADELAVAWJACR-NSHDSACASA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AXAIC50: 7.4 nM (100) BINDINGDB
AXAIC50: 7.4 nM BINDINGMOAD
AXAIC50: 7.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.344α = 90.00
b = 69.384β = 92.35
c = 52.707γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-12-13
    Type: Advisory, Database references