7AVQ | pdb_00007avq

Crystal structure of haspin in complex with disubstituted imidazo[1,2- b]pyridazine inhibitor (compound 12)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.179 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AVQ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design of new disubstituted imidazo[1,2- b ]pyridazine derivatives as selective Haspin inhibitors. Synthesis, binding mode and anticancer biological evaluation.

Elie, J.Feizbakhsh, O.Desban, N.Josselin, B.Baratte, B.Bescond, A.Duez, J.Fant, X.Bach, S.Marie, D.Place, M.Ben Salah, S.Chartier, A.Berteina-Raboin, S.Chaikuad, A.Knapp, S.Carles, F.Bonnet, P.Buron, F.Routier, S.Ruchaud, S.

(2020) J Enzyme Inhib Med Chem 35: 1840-1853

  • DOI: https://doi.org/10.1080/14756366.2020.1825408
  • Primary Citation Related Structures: 
    7AVQ

  • PubMed Abstract: 

    Haspin is a mitotic protein kinase required for proper cell division by modulating Aurora B kinase localisation and activity as well as histone phosphorylation. Here a series of imidazopyridazines based on the CHR-6494 and Structure Activity Relationship was established. An assessment of the inhibitory activity of the lead structures on human Haspin and several other protein kinases is presented. The lead structure was rapidly optimised using a combination of crystal structures and effective docking models, with the best inhibitors exhibiting potent inhibitory activity on Haspin with IC 50 between 6 and 100 nM in vitro . The developed inhibitors displayed anti-proliferative properties against various human cancer cell lines in 2D and spheroid cultures and significantly inhibited the migration ability of osteosarcoma U-2 OS cells. Notably, we show that our lead compounds are powerful Haspin inhibitors in human cells, and did not block G2/M cell cycle transition due to improved selectivity against CDK1/CyclinB.


  • Organizational Affiliation
    • Institut de Chimie Organique et Analytique, Université d'Orléans, UMR CNRS 7311, Orléans Cedex 2, France.

Macromolecule Content 

  • Total Structure Weight: 41.36 kDa 
  • Atom Count: 3,027 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 357 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase haspin357Homo sapiensMutation(s): 0 
Gene Names: HASPINGSG2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens)
Explore Q8TF76 
Go to UniProtKB:  Q8TF76
PHAROS:  Q8TF76
GTEx:  ENSG00000177602 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TF76
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S1Z
(Subject of Investigation/LOI)

Query on S1Z



Download:Ideal Coordinates CCD File
B [auth A](2~{R})-2-[[3-(2~{H}-indazol-5-yl)imidazo[1,2-b]pyridazin-6-yl]amino]butan-1-ol
C17 H18 N6 O
ZGMMFRHRGWCVND-CYBMUJFWSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
F [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.179 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.349α = 90
b = 78.009β = 90
c = 86.15γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references, Structure summary
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description