7KX6

Crystal structure of DCLK1-KD in complex with XMD8-85


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for small molecule targeting of Doublecortin Like Kinase 1 with DCLK1-IN-1.

Patel, O.Roy, M.J.Kropp, A.Hardy, J.M.Dai, W.Lucet, I.S.

(2021) Commun Biol 4: 1105-1105

  • DOI: https://doi.org/10.1038/s42003-021-02631-y
  • Primary Citation of Related Structures:  
    7KX6, 7KX8, 7KXW

  • PubMed Abstract: 

    Doublecortin-like kinase 1 (DCLK1) is an understudied bi-functional kinase with a proven role in tumour growth and development. However, the presence of tissue-specific spliced DCLK1 isoforms with distinct biological functions have challenged the development of effective strategies to understand the role of DCLK1 in oncogenesis. Recently, DCLK1-IN-1 was reported as a highly selective DCLK1 inhibitor, a powerful tool to dissect DCLK1 biological functions. Here, we report the crystal structures of DCLK1 kinase domain in complex with DCLK1-IN-1 and its precursors. Combined, our data rationalises the structure-activity relationship that informed the development of DCLK1-IN-1 and provides the basis for the high selectivity of DCLK1-IN-1, with DCLK1-IN-1 inducing a drastic conformational change of the ATP binding site. We demonstrate that DCLK1-IN-1 binds DCLK1 long isoforms but does not prevent DCLK1's Microtubule-Associated Protein (MAP) function. Together, our work provides an invaluable structural platform to further the design of isoform-specific DCLK1 modulators for therapeutic intervention.


  • Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. patel.o@wehi.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase DCLK1
A, B
280Homo sapiensMutation(s): 0 
Gene Names: DCLK1DCAMKL1DCDC3AKIAA0369
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15075 (Homo sapiens)
Explore O15075 
Go to UniProtKB:  O15075
PHAROS:  O15075
GTEx:  ENSG00000133083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15075
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X7Y (Subject of Investigation/LOI)
Query on X7Y

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one
C25 H29 N7 O2
DDTPGANIPBKTNU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
X7Y BindingDB:  7KX6 Kd: 1.2 (nM) from 1 assay(s)
IC50: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.18α = 90
b = 63.33β = 100.47
c = 152.491γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
Blu-Icedata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1162058

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description