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

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm801166j
  • Primary Citation of Related Structures:  
    3DNG, 3DPE, 3DPF

  • 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 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.

  • 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil collagenase163Homo sapiensMutation(s): 0 
Gene Names: MMP8CLG1
UniProt & NIH Common Fund Data Resources
Find proteins for P22894 (Homo sapiens)
Explore P22894 
Go to UniProtKB:  P22894
PHAROS:  P22894
GTEx:  ENSG00000118113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22894
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AXB

Download Ideal Coordinates CCD File 
F [auth A]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
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
AXB BindingDB:  3DPE IC50: 57 (nM) from 1 assay(s)
PDBBind:  3DPE IC50: 57 (nM) from 1 assay(s)
Binding MOAD:  3DPE IC50: 57 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.29α = 90
b = 68.95β = 105.41
c = 32.75γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description