1ZP5

Crystal structure of the complex between MMP-8 and a N-hydroxyurea inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

N-Hydroxyurea as zinc binding group in matrix metalloproteinase inhibition: Mode of binding in a complex with MMP-8.

Campestre, C.Agamennone, M.Tortorella, P.Preziuso, S.Biasone, A.Gavuzzo, E.Pochetti, G.Mazza, F.Hiller, O.Tschesche, H.Consalvi, V.Gallina, C.

(2006) Bioorg Med Chem Lett 16: 20-24

  • DOI: https://doi.org/10.1016/j.bmcl.2005.09.057
  • Primary Citation of Related Structures:  
    1ZP5

  • PubMed Abstract: 

    The first crystallographic structure of an N-hydroxyurea inhibitor bound into the active site of a matrix metalloproteinase is reported. The ligand and three other analogues were prepared and studied as inhibitors of MMP-2, MMP-3, and MMP-8. The crystal structure of the complex with MMP-8 shows that the N-hydroxyurea, contrary to the analogous hydroxamate, binds the catalytic zinc ion in a monodentate rather than bidentate mode and with high out-of-plane distortion of the amide bonds.


  • Organizational Affiliation

    Dipartimento di Scienze del Farmaco, Università degli Studi 'G. d'Annunzio', Chieti, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil collagenase163Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
2NI Binding MOAD:  1ZP5 IC50: 1.20e+6 (nM) from 1 assay(s)
BindingDB:  1ZP5 IC50: 1.20e+6 (nM) from 1 assay(s)
PDBBind:  1ZP5 IC50: 1.20e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.387α = 90
b = 52.675β = 90
c = 67.331γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Database references
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description