3DNG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.220 

Starting Model: experimental
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This is version 1.3 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: 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil collagenase
A, B
163Homo sapiensMutation(s): 0 
Gene Names: MMP8CLG1
EC: 3.4.24.34
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AXA
Query on AXA

Download Ideal Coordinates CCD File 
G [auth A],
L [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AXA BindingDB:  3DNG IC50: 7.4 (nM) from 1 assay(s)
PDBBind:  3DNG IC50: 7.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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
b = 69.384β = 92.35
c = 52.707γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
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: Advisory, Database references
  • Version 1.3: 2023-11-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description