7NCF

Crystal structure of HIPK2 in complex with MU135 (compound 21e)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Highly selective inhibitors of protein kinases CLK and HIPK with the furo[3,2-b]pyridine core.

Nemec, V.Maier, L.Berger, B.T.Chaikuad, A.Drapela, S.Soucek, K.Knapp, S.Paruch, K.

(2021) Eur J Med Chem 215: 113299-113299

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113299
  • Primary Citation of Related Structures:  
    7NCF

  • PubMed Abstract: 

    The furo [3,2-b]pyridine motif represents a relatively underexplored central pharmacophore in the area of kinase inhibitors. Herein, we report flexible synthesis of 3,5-disubstituted furo [3,2-b]pyridines that relies on chemoselective couplings of newly prepared 5-chloro-3-iodofuro [3,2-b]pyridine. This methodology allowed efficient second-generation synthesis of the state-of-the-art chemical biology probe for CLK1/2/4 MU1210, and identification of the highly selective inhibitors of HIPKs MU135 and MU1787 which are presented and characterized in this study, including the X-ray crystal structure of MU135 in HIPK2. chemical biology probe.


  • Organizational Affiliation

    Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, Pekařská 53, 656 91, Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homeodomain-interacting protein kinase 2367Homo sapiensMutation(s): 0 
Gene Names: HIPK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X6 (Homo sapiens)
Explore Q9H2X6 
Go to UniProtKB:  Q9H2X6
PHAROS:  Q9H2X6
GTEx:  ENSG00000064393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2X6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U82 (Subject of Investigation/LOI)
Query on U82

Download Ideal Coordinates CCD File 
B [auth A]3-(4-Tert-butylphenyl)-5-(1H-pyrazol-4-yl)furo[3,2-b]pyridine
C20 H19 N3 O
OOLXXVMFVSTNLJ-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
U82 BindingDB:  7NCF IC50: min: 119, max: 476 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.855α = 90
b = 133.855β = 90
c = 56.771γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata 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: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description