7OVY

Crystal structure of a dimeric based inhibitor JG34 in complex with the MMP-12 catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Dimeric Arylsulfonamides as Potent ADAM8 Inhibitors.

Cuffaro, D.Camodeca, C.Tuccinardi, T.Ciccone, L.Bartsch, J.W.Kellermann, T.Cook, L.Nuti, E.Rossello, A.

(2021) ACS Med Chem Lett 12: 1787-1793

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00411
  • Primary Citation of Related Structures:  
    7OVY

  • PubMed Abstract: 

    The metalloproteinase ADAM8 is upregulated in several cancers but has a dispensable function under physiological conditions. In tumor cells, ADAM8 is involved in invasion, migration, and angiogenesis. The use of bivalent inhibitors could impair migration and invasion through the double binding to a homodimeric form of ADAM8 located on the cell surface of tumor cells. Herein we report the rational design and synthesis of the first dimeric ADAM8 inhibitors selective over ADAM10 and matrix metalloproteinases. Bivalent derivatives have been obtained by dimerizing the structure of a previously described ADAM17 inhibitor, JG26. In particular, derivative 2 was shown to inhibit ADAM8 proteolytic activity in vitro and in cell-based assays at nanomolar concentration. Moreover, it was more effective than the parent monomeric compound in blocking invasiveness in the breast cancer MDA-MB-231 cell line, thus supporting our hypothesis about the importance of inhibiting the active homodimer of ADAM8.


  • 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
Macrophage metalloelastase159Homo sapiensMutation(s): 1 
Gene Names: MMP12HME
EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
GTEx:  ENSG00000262406 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2IF (Subject of Investigation/LOI)
Query on 2IF

Download Ideal Coordinates CCD File 
G [auth A]~{N}1,~{N}3-bis[4-[[(4~{R})-4-[[4-[[3,5-bis(bromanyl)phenyl]methoxy]phenyl]sulfonylamino]-5-(oxidanylamino)-5-oxidanylidene-pentyl]amino]-4-oxidanylidene-butyl]benzene-1,3-dicarboxamide
C52 H58 Br4 N8 O14 S2
JQLHAXGMYALIFJ-AWSIMMLFSA-N
PGR (Subject of Investigation/LOI)
Query on PGR

Download Ideal Coordinates CCD File 
I [auth A]R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2IF BindingDB:  7OVY IC50: 242 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 60.45β = 115.24
c = 54.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description