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 collagenaseA, B163Homo sapiensMutation(s): 0 
Gene Names: MMP8, CLG1
EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens)
Explore P22894 
Go to UniProtKB:  P22894
NIH Common Fund Data Resources
PHAROS  P22894
GTEx  ENSG00000118113
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AXB
Query on AXB
Download Ideal Coordinates 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 Ideal Coordinates CCD File 
A
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates 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

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View more in-depth experimental data

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