4HGT

Crystal structure of ck1d with compound 13

• PDB DOI:  https://doi.org/10.2210/pdb4HGT/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-08 Released: 2012-11-21 
• Deposition Author(s): Huang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.240 

Literature

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

• PubMed: 24900428 
• 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.

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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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.47 kDa 
• Atom Count: 5,160 
• Modelled Residue Count: 563 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A, B	296	Homo sapiens	Mutation(s): 0  Gene Names: CSNK1D, HCKID 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15G	C [auth A], D [auth B]	2-{2-[(3,4-difluorophenoxy)methyl]-5-methoxypyridin-4-yl}-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one C20 H17 F2 N3 O3 GMIKNOQZLHKCFH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
15G	PDBBind:  4HGT	IC50: 40 (nM) from 1 assay(s)
	BindingDB:  4HGT	IC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.240 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.17	α = 90
b = 72.97	β = 103.63
c = 89.33	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references