6RCG | pdb_00006rcg

Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor

PDB DOI: https://doi.org/10.2210/pdb6RCG/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-11 Released: 2020-03-25
Deposition Author(s): Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Roush, W.R., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.185 (Depositor), 0.187 (DCC)
R-Value Work:
0.142 (Depositor), 0.142 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor

Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Roush, W.R., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 35.03 kDa
Atom Count: 2,915
Modeled Residue Count: 295
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A	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 GTEx: ENSG00000141551
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48730
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K0E Query on K0E Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	~{N}-[[6,7-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(3-fluorophenyl)-2-morpholin-4-yl-purin-6-amine C₂₃ H₁₉ F₃ N₈ O CEBMEQPREMCWOL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.185 (Depositor), 0.187 (DCC)
R-Value Work: 0.142 (Depositor), 0.142 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.04	α = 90
b = 53.55	β = 113.45
c = 72.17	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2020-03-25
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.