6I18

CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH BDP-13176


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H0NClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents.

Francis, S.Croft, D.Schuttelkopf, A.W.Parry, C.Pugliese, A.Cameron, K.Claydon, S.Drysdale, M.Gardner, C.Gohlke, A.Goodwin, G.Gray, C.H.Konczal, J.McDonald, L.Mezna, M.Pannifer, A.Paul, N.R.Machesky, L.McKinnon, H.Bower, J.

(2019) Bioorg Med Chem Lett 29: 1023-1029

  • DOI: https://doi.org/10.1016/j.bmcl.2019.01.035
  • Primary Citation of Related Structures:  
    6I0Z, 6I10, 6I11, 6I12, 6I13, 6I14, 6I15, 6I16, 6I17, 6I18

  • PubMed Abstract: 

    Fascin is an actin binding and bundling protein that is not expressed in normal epithelial tissues but overexpressed in a variety of invasive epithelial tumors. It has a critical role in cancer cell metastasis by promoting cell migration and invasion. Here we report the crystal structures of fascin in complex with a series of novel and potent inhibitors. Structure-based elaboration of these compounds enabled the development of a series with nanomolar affinities for fascin, good physicochemical properties and the ability to inhibit fascin-mediated bundling of filamentous actin. These compounds provide promising starting points for fascin-targeted anti-metastatic therapies.


  • Organizational Affiliation

    Drug Discovery Unit, CRUK Beatson Institute, Glasgow G61 1BD, UK. Electronic address: s.francis@beatson.gla.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fascin493Homo sapiensMutation(s): 0 
Gene Names: FSCN1FAN1HSNSNL
UniProt & NIH Common Fund Data Resources
Find proteins for Q16658 (Homo sapiens)
Explore Q16658 
Go to UniProtKB:  Q16658
PHAROS:  Q16658
GTEx:  ENSG00000075618 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16658
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H0N (Subject of Investigation/LOI)
Query on H0N

Download Ideal Coordinates CCD File 
H [auth A]5-[(3,4-dichlorophenyl)methyl]-4-oxidanylidene-1-piperidin-4-yl-~{N}-pyridin-4-yl-pyrazolo[4,3-c]pyridine-7-carboxamide
C24 H22 Cl2 N6 O2
BMOUOZDRMBLNSI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
H0N BindingDB:  6I18 Kd: min: 50, max: 90 (nM) from 2 assay(s)
IC50: 240 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.66α = 90
b = 87.81β = 90
c = 98.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H0NClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description