1ZP5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 

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

  • 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: 
    • 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
    • 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
    • Hydroxamic acids as pharmacological agents.
      Muri, E.M.,Nieto, M.J.,Sindelar, R.D.,Williamson, J.S.
      (2002) Curr.Med.Chem. 9: 1631


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil collagenase
A
163Homo sapiensMutation(s): 0 
Gene Names: MMP8 (CLG1)
EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens)
Go to Gene View: MMP8
Go to UniProtKB:  P22894
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2NI
Query on 2NI

Download SDF File 
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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2NIIC50: 1200000 nM (100) BINDINGDB
2NIIC50: 1200000 nM BINDINGMOAD
2NIIC50: 1200000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.387α = 90.00
b = 52.675β = 90.00
c = 67.331γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references