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 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 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 crys ...

    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.


    Related Citations: 
    • Hydroxamic acids as pharmacological agents.
      Muri, E.M., Nieto, M.J., Sindelar, R.D., Williamson, J.S.
      (2002) Curr Med Chem 9: 1631
    • Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor.
      Grams, F., Crimmin, M., Hinnes, L., Huxley, P., Pieper, M., Tschesche, H., Bode, W.
      (1995) Biochemistry 34: 14012
    • Discovery of potent non peptide inhibitors of stromelysin using SAR by NMR.
      Hajduck, P.J., Sheppard, G., Nettesheim, D.G., Olejniczak, E.T., Shuker, S.B., Meadows, R.P., Steinman, D.H., Carrera, G.M., Marcotte, P.A., Severin, J., Walter, K., Smith, H., Gubbins, E., Simmer, R., Holzman, T.F., Morgan, D.W., Davidsen, S.K., Summers, J.B., Fesik, S.W.
      (1997) J Am Chem Soc 119: 5818
    • Biaryl ether retrohydroxamates as potent, long-lived, orally bioavailable MMP inhibitors.
      Michaelides, M.R., Dellaria, J.F., Gong, J., Holms, J.H., Bouska, J.J., Stacey, J., Wada, C.K., Heyman, H.R., Curtin, M.L., Guo, Y., Goodfellow, C.L., Elmore, I.B., Albert, D.H., Magoc, T.J., Marcotte, P.A., Morgan, D.W., Davidsen, S.K.
      (2001) Bioorg Med Chem Lett 11: 1553

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil collagenaseA163Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NI
Query on 2NI

Download CCD File 
A
N-{2-[(4'-CYANO-1,1'-BIPHENYL-4-YL)OXY]ETHYL}-N'-HYDROXY-N-METHYLUREA
C17 H17 N3 O3
GVMUNGGWXRKCEU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2NIIC50:  1200000   nM  Binding MOAD
2NIIC50 :  1200000   nM  PDBBind
2NIIC50:  1200000   nM  BindingDB
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



Entry History 

Deposition Data

Revision History 

  • 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