5I12

Crystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors.

Nuti, E.Cuffaro, D.D'Andrea, F.Rosalia, L.Tepshi, L.Fabbi, M.Carbotti, G.Ferrini, S.Santamaria, S.Camodeca, C.Ciccone, L.Orlandini, E.Nencetti, S.Stura, E.A.Dive, V.Rossello, A.

(2016) ChemMedChem 11: 1626-1637

  • DOI: https://doi.org/10.1002/cmdc.201600235
  • Primary Citation of Related Structures:  
    5I0L, 5I12, 5I2Z, 5I3M, 5I43, 5I4O

  • PubMed Abstract: 

    Matrix metalloproteinase-12 (MMP-12) can be considered an attractive target to study selective inhibitors useful in the development of new therapies for lung and cardiovascular diseases. In this study, a new series of arylsulfonamide carboxylates, with increased hydrophilicity resulting from conjugation with a β-N-acetyl-d-glucosamine moiety, were designed and synthesized as MMP-12 selective inhibitors. Their inhibitory activity was evaluated on human MMPs by using the fluorimetric assay, and a crystallographic analysis was performed to characterize their binding mode. Among these glycoconjugates, a nanomolar MMP-12 inhibitor with improved water solubility, compound 3 [(R)-2-(N-(2-(3-(2-acetamido-2-deoxy-β-d-glucopyranosyl)thioureido)ethyl)biphenyl-4-ylsulfonamido)-3-methylbutanoic acid], was identified.


  • Organizational Affiliation

    Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-9,Matrix metalloproteinase-9157Homo sapiensMutation(s): 0 
Gene Names: MMP9CLG4B
EC: 3.4.24.35
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
PHAROS:  P14780
GTEx:  ENSG00000100985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H27
Query on H27

Download Ideal Coordinates CCD File 
G [auth A](2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}carbamothioyl)amino]ethenyl}(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid
C34 H42 N4 O12 S2
NIEQAOCPXJWQAU-NPCCVVQBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.56α = 90
b = 39.56β = 90
c = 163.55γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description