1ZVX

Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (R-enantiomer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural insight into the stereoselective inhibition of MMP-8 by enantiomeric sulfonamide phosphonates.

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

(2006) J.Med.Chem. 49: 923-931

  • DOI: 10.1021/jm050787+
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Potent and selective inhibitors of matrix metalloproteinases (MMPs), a family of zinc proteases that can degrade all the components of the extracellular matrix, could be useful for treatment of diseases such as cancer and arthritis. The most potent M ...

    Potent and selective inhibitors of matrix metalloproteinases (MMPs), a family of zinc proteases that can degrade all the components of the extracellular matrix, could be useful for treatment of diseases such as cancer and arthritis. The most potent MMP inhibitors are based on hydroxamate as zinc-binding group (ZBG). alpha-Arylsulfonylamino phosphonates incorporate a particularly favorable combination of phosphonate as ZBG and arylsulfonylamino backbone so that their affinity exceptionally attains the nanomolar strength frequently observed for hydroxamate analogues. The detailed mode of binding of [1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl]phosphonate has been clarified by the crystal structures of the complexes that the R- and S-enantiomers respectively form with MMP-8. The reasons for the preferential MMP-8 inhibition by the R-phosphonate are underlined and the differences in the mode of binding of analogous alpha-arylsulfonylamino hydroxamates and carboxylates are discussed.


    Related Citations: 
    • X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: implications for inhibitor selectivity
      Pavlovsky, A.G.,Williams, M.G.,Ye, Q.Z.,Ortwine, D.F.,Purchase II, C.F.,White, A.D.,Dhanaraj, V.,Roth, B.D.,Johnson, L.L.,Hupe, D.,Humblet, C.,Blundell, T.L.
      (1999) Protein Sci. 8: 1455
    • X-ray structuresof human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design
      Grams, F.,Reinemer, P.,Powers, J.C.,Kleine, T.,Pieper, M.,Tschesche, H.,Huber, R.,Bode, W.
      (1995) Eur.J.Biochem. 228: 830
    • Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design
      Gavuzzo, E.,Pochetti, G.,Mazza, F.,Gallina, C.,Gorini, B.,D'Alessio, S.,Pieper, M.,Tschesche, H.,Tucker, P.A.
      (2000) J.Med.Chem. 43: 3377


    Organizational Affiliation

    Istituto di Cristallografia, C.N.R., Monterotondo Stazione, Rome, 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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FIN
Query on FIN

Download SDF File 
Download CCD File 
A
(1R)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID
C17 H22 N O6 P S
BZVYQWLRCHLAGK-QGZVFWFLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FINKi: 0.6 nM (100) BINDINGDB
FINIC50: 1.4 nM (100) BINDINGDB
FINKi: 0.6 nM BINDINGMOAD
FINKi: 0.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.706α = 90.00
b = 54.754β = 90.00
c = 68.413γ = 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: 2006-05-16
    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: Advisory, Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references