Crystal structure of ck1d with compound 13

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Work: 0.240 

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Structure-Based Design of Potent and Selective CK1 gamma Inhibitors.

Huang, H.Acquaviva, L.Berry, V.Bregman, H.Chakka, N.O'Connor, A.DiMauro, E.F.Dovey, J.Epstein, O.Grubinska, B.Goldstein, J.Gunaydin, H.Hua, Z.Huang, X.Huang, L.Human, J.Long, A.Newcomb, J.Patel, V.F.Saffran, D.Serafino, R.Schneider, S.Strathdee, C.Tang, J.Turci, S.White, R.Yu, V.Zhao, H.Wilson, C.Martin, M.W.

(2012) ACS Med Chem Lett 3: 1059-1064

  • DOI: https://doi.org/10.1021/ml300278f
  • Primary Citation of Related Structures:  
    4HGL, 4HGT

  • PubMed Abstract: 

    Aberrant activation of the Wnt pathway is believed to drive the development and growth of some cancers. The central role of CK1γ in Wnt signal transduction makes it an attractive target for the treatment of Wnt-pathway dependent cancers. We describe a structure-based approach that led to the discovery of a series of pyridyl pyrrolopyridinones as potent and selective CK1γ inhibitors. These compounds exhibited good enzyme and cell potency, as well as selectivity against other CK1 isoforms. A single oral dose of compound 13 resulted in significant inhibition of LRP6 phosphorylation in a mouse tumor PD model.

  • Organizational Affiliation

    Departments of Medicinal Chemistry; Pharmacokinetics and Drug Metabolism; Oncology Research; and Molecular Structure, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform delta
A, B
296Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 15G

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H17 F2 N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
15G BindingDB:  4HGT IC50: 40 (nM) from 1 assay(s)
PDBBind:  4HGT IC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.17α = 90
b = 72.97β = 103.63
c = 89.33γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2012-11-21 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations