4TN6 | pdb_00004tn6

CK1d in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb4TN6/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-06-03 Released: 2015-08-12
Deposition Author(s): Liu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.239 (Depositor), 0.244 (DCC)
R-Value Work:
0.187 (Depositor), 0.194 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CK1D IN COMPLEX WITH inhibitor

Liu, S.

To be published.

Macromolecule Content

Total Structure Weight: 74.42 kDa
Atom Count: 5,001
Modeled Residue Count: 577
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform delta	A, B	318	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
PFO Query on PFO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-{4-(4-fluorophenyl)-1-[1-(1,2-oxazol-3-ylmethyl)piperidin-4-yl]-1H-imidazol-5-yl}pyrimidin-2-amine C₂₂ H₂₂ F N₇ O XPWHRQHBPRSUAW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth B] H [auth B] D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.239 (Depositor), 0.244 (DCC)
R-Value Work: 0.187 (Depositor), 0.194 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.487	α = 90
b = 115.336	β = 109.27
c = 61.533	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Liu, S.

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

4TN6 | pdb_00004tn6

CK1d in complex with inhibitor

Literature

CK1D IN COMPLEX WITH inhibitor

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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