3UYT

crystal structure of ck1d with PF670462 from P1 crystal form

PDB DOI: https://doi.org/10.2210/pdb3UYT/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-12-06 Released: 2012-01-11
Deposition Author(s): Huang, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.244

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the interaction between casein kinase 1 delta and a potent and selective inhibitor.

Long, A., Zhao, H., Huang, X.

(2012) J Med Chem 55: 956-960

PubMed: 22168824 Search on PubMed
DOI: https://doi.org/10.1021/jm201387s
Primary Citation of Related Structures:
3UYS, 3UYT, 3UZP

PubMed Abstract:
Casein kinase 1 delta (CK1δ) and its closest homologue CK1ε are key regulators of diverse cellular growth and survival processes such as Wnt signaling, DNA repair, and circadian rhythms. We report three crystal structures of the kinase domain of human CK1δ, one apo and two complexed with a potent and selective CK1δ/ε inhibitor PF670462 in two different crystal forms. These structures provide a molecular basis for the strong and specific inhibitor interactions and suggest clues for further development of CK1δ/ε inhibitors.

Organizational Affiliation

Department of Molecular Structure, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States.

Macromolecule Content

Total Structure Weight: 139.42 kDa
Atom Count: 10,156
Modelled Residue Count: 1,127
Deposited Residue Count: 1,184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A, B, C, D	296	Homo sapiens	Mutation(s): 0 Gene Names: CSNK1D EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (UniProt)
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48730
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0CK Query on 0CK Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], J [auth C], M [auth D]	4-[1-cyclohexyl-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine C₁₉ H₂₀ F N₅ WUDBUIUHVNECTM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	F [auth A] G [auth A] I [auth B] K [auth C] L [auth C] F [auth A], G [auth A], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
0CK	BindingDB: 3UYT	IC50: min: 7.7, max: 130 (nM) from 14 assay(s)
0CK	PDBBind: 3UYT	IC50: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.244
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.15	α = 72.87
b = 85.34	β = 74.36
c = 89.14	γ = 87.26

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Huang, X.

Revision History (Full details and data files)

Version 1.0: 2012-01-11
Type: Initial release
Version 1.1: 2012-11-14
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations