6I5I | pdb_00006i5i

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.196 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.164 (Depositor) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6I5I

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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 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.


  • Organizational Affiliation
    • Department of Chemistry, CZ-Openscreen, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 40.68 kDa 
  • Atom Count: 3,178 
  • Modeled Residue Count: 335 
  • Deposited Residue Count: 339 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity protein kinase CLK1339Homo sapiensMutation(s): 1 
Gene Names: CLK1CLK
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
GTEx:  ENSG00000013441 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49759
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H3E

Query on H3E



Download:Ideal Coordinates CCD File
B [auth A]5-(1-methylpyrazol-4-yl)-3-[1-(phenylmethyl)pyrazol-4-yl]furo[3,2-b]pyridine
C21 H17 N5 O
IAJZCWZPVNGTMZ-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]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.196 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.164 (Depositor) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.96α = 90
b = 64.01β = 122.71
c = 81.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description