3DPF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 

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:  
    3DPE, 3DPF, 3DNG

  • 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
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil collagenaseAB163Homo sapiensMutation(s): 0 
Gene Names: MMP8CLG1
EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens)
Explore P22894 
Go to UniProtKB:  P22894
NIH Common Fund Data Resources
PHAROS  P22894
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AXB
Query on AXB

Download CCD File 
A, B
N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide
C24 H21 N5 O6 S2
QHDIXGPUTSAIJX-UHFFFAOYSA-N
 Ligand Interaction
HAE
Query on HAE

Download CCD File 
A
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AXBIC50 :  57   nM  PDBBind
AXBIC50:  57   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 69.21β = 90
c = 81.23γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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