6I5L

Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN316 (derivative of compound 12h)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Literature

Furo[3,2-b]pyridine: A Privileged Scaffold for Highly Selective Kinase Inhibitors and Effective Modulators of the Hedgehog Pathway.

Nemec, V., Hylsova, M., Maier, L., Flegel, J., Sievers, S., Ziegler, S., Schroder, M., Berger, B.T., Chaikuad, A., Valcikova, B., Uldrijan, S., Drapela, S., Soucek, K., Waldmann, H., Knapp, S., Paruch, K.

(2019) Angew Chem Int Ed Engl 58: 1062-1066

  • DOI: https://doi.org/10.1002/anie.201810312
  • Primary Citation of Related Structures:  
    6I5H, 6I5I, 6I5K, 6I5L

  • PubMed Abstract: 

    • Reported is the identification of the furo[3,2-b]pyridine core as a novel scaffold for potent and highly selective inhibitors of cdc-like kinases (CLKs) and efficient modulators of the Hedgehog signaling pathway. Initially, a diverse target compound set was prepared by synthetic sequences based on chemoselective metal-mediated couplings, including assembly of the furo[3,2-b]pyridine scaffold by copper-mediated oxidative cyclization ...

    Reported is the identification of the furo[3,2-b]pyridine core as a novel scaffold for potent and highly selective inhibitors of cdc-like kinases (CLKs) and efficient modulators of the Hedgehog signaling pathway. Initially, a diverse target compound set was prepared by synthetic sequences based on chemoselective metal-mediated couplings, including assembly of the furo[3,2-b]pyridine scaffold by copper-mediated oxidative cyclization. Optimization of the subseries containing 3,5-disubstituted furo[3,2-b]pyridines afforded potent, cell-active, and highly selective inhibitors of CLKs. Profiling of the kinase-inactive subset of 3,5,7-trisubstituted furo[3,2-b]pyridines revealed sub-micromolar modulators of the Hedgehog pathway.

    Organizational Affiliation: 

    International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1
A, B, C
339Homo sapiensMutation(s): 1 
Gene Names: CLK1, CLK
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens)
Explore P49759 
Go to UniProtKB:  P49759
PHAROS:  P49759
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49759
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H3Q
Query on H3Q
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C]		3-(3-cyclobutylphenyl)-5-(1-methylpyrazol-4-yl)furo[3,2-b]pyridine
C21 H19 N3 O
DDWOGFZIVMALPO-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B],
L [auth C]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
N [auth C]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
N [auth C],
O [auth C],
P [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.129α = 90
b = 117.55β = 99.1
c = 92.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references