5IXB

Structure of human Melanoma Inhibitory Activity (MIA) Protein in complex with Pyrimidin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Small Molecules Antagonise the MIA-Fibronectin Interaction in Malignant Melanoma.

Yip, K.T.Zhong, X.Y.Seibel, N.Putz, S.Autzen, J.Gasper, R.Hofmann, E.Scherkenbeck, J.Stoll, R.

(2016) Sci Rep 6: 25119-25119

  • DOI: 10.1038/srep25119
  • Primary Citation of Related Structures:  
    5IXB

  • PubMed Abstract: 
  • Melanoma inhibitory activity (MIA), an extracellular protein highly expressed by malignant melanoma cells, plays an important functional role in melanoma development, progression, and metastasis. After its secretion, MIA directly interacts with extracellular matrix proteins, such as fibronectin (FN) ...

    Melanoma inhibitory activity (MIA), an extracellular protein highly expressed by malignant melanoma cells, plays an important functional role in melanoma development, progression, and metastasis. After its secretion, MIA directly interacts with extracellular matrix proteins, such as fibronectin (FN). By this mechanism, MIA actively facilitates focal cell detachment from surrounding structures and strongly promotes tumour cell invasion and migration. Hence, the molecular understanding of MIA's function provides a promising target for the development of new strategies in malignant melanoma therapy. Here, we describe for the first time the discovery of small molecules that are able to disrupt the MIA-FN complex by selectively binding to a new druggable pocket, which we could identify on MIA by structural analysis and fragment-based screening. Our findings may inspire novel drug discovery efforts aiming at a therapeutically effective treatment of melanoma by targeting MIA.


    Organizational Affiliation

    Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Melanoma-derived growth regulatory proteinA, B108Homo sapiensMutation(s): 0 
Gene Names: MIA
UniProt & NIH Common Fund Data Resources
Find proteins for Q16674 (Homo sapiens)
Explore Q16674 
Go to UniProtKB:  Q16674
PHAROS:  Q16674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16674
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LGA
Query on LGA

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PYRIMIDIN-2-AMINE
C4 H5 N3
LJXQPZWIHJMPQQ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.44α = 90
b = 47.48β = 90
c = 87.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release