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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil collagenase163Homo sapiensMutation(s): 0 
Gene Names: MMP8, CLG1
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22894
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NI
Query on 2NI
Download Ideal Coordinates CCD File 
F [auth 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 Ideal Coordinates CCD File 
D [auth A],
E [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2NI Binding MOAD:  1ZP5 IC50: 1.20e+6 (nM) from 1 assay(s)
PDBBind:  1ZP5 IC50: 1.20e+6 (nM) from 1 assay(s)
BindingDB:  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

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Ligand Structure Quality Assessment 


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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