7O9Y | pdb_00007o9y

Crystal structure of di-phosphorylated human CLK1 in complex with 4-(1H-indol-3-yl)pyrimidin-2-amine

PDB DOI: https://doi.org/10.2210/pdb7O9Y/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-18 Released: 2022-05-04
Deposition Author(s): Livnah, O., Domovich, Y., Bracher, F., Aiger, C.
Funding Organization(s): German-Israeli Foundation for Research and Development

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (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

Development of novel CLK1 inhibitors as potential drugs for treatment of Chikungunya virus infections

Livnah, O., Domovich, Y., Bracher, F., Aiger, C.

To be published.

Macromolecule Content

Total Structure Weight: 39.66 kDa
Atom Count: 2,908
Modeled Residue Count: 330
Deposited Residue Count: 337
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A	337	Homo sapiens	Mutation(s): 0 Gene Names: CLK1, CLK EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens) Explore P49759 Go to UniProtKB: P49759
PHAROS: P49759 GTEx: ENSG00000013441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V5T (Subject of Investigation/LOI) Query on V5T Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(1~{H}-indol-3-yl)pyrimidin-2-amine C₁₂ H₁₀ N₄ QNMZWFNNJMGJPU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
V5T	BindingDB: 7O9Y	IC50: 530 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.43	α = 90
b = 68.43	β = 90
c = 284.45	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Funding Organization	Location	Grant Number
German-Israeli Foundation for Research and Development	Israel	i-1453-207.9/2018

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.