1ZS0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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:  
    1ZS0, 1ZVX

  • 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
    • 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
    • X-ray structures of 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

    Organizational Affiliation

    Istituto di Cristallografia, C.N.R., Monterotondo Stazione, Rome, 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EIN
Query on EIN

Download CCD File 
A
(1S)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID
C17 H22 N O6 P S
BZVYQWLRCHLAGK-KRWDZBQOSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-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 %)
EINIC50:  810   nM  BindingDB
EINKi:  700   nM  BindingDB
EINKi:  700   nM  Binding MOAD
EINKi :  700   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.062α = 90
b = 67.884β = 90
c = 70.517γ = 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: 2006-05-02
    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