7NZY

Crystal structure of human Casein Kinase I delta in complex with CGS-15943


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Phenotypic Discovery of Triazolo[1,5- c ]quinazolines as a First-In-Class Bone Morphogenetic Protein Amplifier Chemotype.

Wesseler, F.Lohmann, S.Riege, D.Halver, J.Roth, A.Pichlo, C.Weber, S.Takamiya, M.Muller, E.Ketzel, J.Flegel, J.Gihring, A.Rastegar, S.Bertrand, J.Baumann, U.Knippschild, U.Peifer, C.Sievers, S.Waldmann, H.Schade, D.

(2022) J Med Chem 65: 15263-15281

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01199
  • Primary Citation of Related Structures:  
    7NZY

  • PubMed Abstract: 

    Phenotypic drug discovery (PDD) continues to fuel the research and development pipelines with first-in-class therapeutic modalities, but success rates critically depend on the quality of the underlying model system. Here, we employed a stem cell-based approach for the target-agnostic, yet pathway-centric discovery of small-molecule cytokine signaling activators to act as morphogens during development and regeneration. Unbiased screening identified triazolo[1,5- c ]quinazolines as a new-in-class in vitro and in vivo active amplifier of the bone morphogenetic protein (BMP) pathway. Cellular BMP outputs were stimulated via enhanced and sustained availability of BMP-Smad proteins, strictly dependent on a minimal BMP input. Holistic target deconvolution unveiled a unique mechanism of dual targeting of casein kinase 1 and phosphatidyl inositol 3-kinase isoforms as key effectors for efficient amplification of osteogenic BMP signaling. This work underscores the asset of PDD to discover unrecognized polypharmacology signatures, in this case significantly expanding the chemical and druggable space of BMP modulators.


  • Organizational Affiliation

    Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B, C, D
314Homo sapiensMutation(s): 0 
Gene Names: CSNK1DHCKID
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48730 (Homo sapiens)
Explore P48730 
Go to UniProtKB:  P48730
PHAROS:  P48730
GTEx:  ENSG00000141551 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48730
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UX2 (Subject of Investigation/LOI)
Query on UX2

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
9-chloranyl-2-(furan-2-yl)-[1,2,4]triazolo[1,5-c]quinazolin-5-amine
C13 H8 Cl N5 O
MSJODEOZODDVGW-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
N [auth D],
O [auth D]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth B],
K [auth C],
L [auth C],
P [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B, C, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.938α = 87.097
b = 82.081β = 74.264
c = 89.556γ = 86.332
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
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: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Refinement description