5UNP | pdb_00005unp

Structure of CDC2-Like Kinase 2 (CLK2) in Complex with Compound T-025 [N2-methyl-N4-(pyrimidin-2-ylmethyl)-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine]

PDB DOI: https://doi.org/10.2210/pdb5UNP/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-01-31 Released: 2018-05-09
Deposition Author(s): Klein, M.G., Tjhen, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.234 (Depositor), 0.237 (DCC)
R-Value Work:
0.201 (Depositor), 0.202 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

A novel CLK inhibitor exhibits anti-tumor efficacies via modulating pre-mRNA splicing and targeting a MYC-dependent vulnerability

Iwai, K., Yaguchi, M., Klein, M.G.

(2018) EMBO Mol Med

Macromolecule Content

Total Structure Weight: 87.51 kDa
Atom Count: 5,824
Modeled Residue Count: 694
Deposited Residue Count: 738
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK2	A, B	369	Homo sapiens	Mutation(s): 0 Gene Names: CLK2 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49760 (Homo sapiens) Explore P49760 Go to UniProtKB: P49760
PHAROS: P49760 GTEx: ENSG00000176444
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8FY Query on 8FY Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N~2~-methyl-N~4~-[(pyrimidin-2-yl)methyl]-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine C₂₁ H₁₈ N₈ PMWVYONICYRLNY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
8FY	BindingDB: 5UNP	Kd: 0.1 (nM) from 1 assay(s)
8FY	BindingDB: 5UNP	IC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free: 0.234 (Depositor), 0.237 (DCC)
R-Value Work: 0.201 (Depositor), 0.202 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.252	α = 90
b = 141.252	β = 90
c = 124.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2024-03-06
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.