6I5H

Crystal structure of CLK1 in complex with furanopyrimidin VN412

• PDB DOI:  https://doi.org/10.2210/pdb6I5H/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-11-13 Released: 2019-01-16 
• Deposition Author(s): Schroeder, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Paruch, K., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.206 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

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

• PubMed: 30569600 
• 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.35 kDa 
• Atom Count: 2,942 
• Modelled Residue Count: 325 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A	339	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H3N (Subject of Investigation/LOI)	H [auth A]	5-(1-methylpyrazol-4-yl)-3-(3-phenoxyphenyl)furo[3,2-b]pyridine C23 H17 N3 O2 RDHFKBABHOAOCH-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.206 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.219	α = 90
b = 64.049	β = 111.99
c = 83.535	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Schroeder, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Paruch, K., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references