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), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (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

View Full Validation Report

Ligand Structure Quality Assessment

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

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.