1ZS0 | pdb_00001zs0

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 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/jm050787+
  • Primary Citation 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 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.


  • Organizational Affiliation
    • Istituto di Cristallografia, C.N.R., Monterotondo Stazione, Rome, Italy.

Macromolecule Content 

  • Total Structure Weight: 18.92 kDa 
  • Atom Count: 1,568 
  • Modeled Residue Count: 163 
  • Deposited Residue Count: 163 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neutrophil collagenase163Homo sapiensMutation(s): 0 
Gene Names: MMP8CLG1
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
GTEx:  ENSG00000118113 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22894
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EIN

Query on EIN



Download:Ideal Coordinates CCD File
F [auth A](1S)-1-{[(4'-METHOXY-1,1'-BIPHENYL-4-YL)SULFONYL]AMINO}-2-METHYLPROPYLPHOSPHONIC ACID
C17 H22 N O6 P S
BZVYQWLRCHLAGK-KRWDZBQOSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
G [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.235 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description