7F3G | pdb_00007f3g

Crystal structure of DCLK1 kinase domain in complex with ruxolitinib

PDB DOI: https://doi.org/10.2210/pdb7F3G/pdb

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

Deposited: 2021-06-16 Released: 2021-08-18
Deposition Author(s): Lim, H.J., Jang, D.M., Kim, H.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.210 (Depositor), 0.217 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis of Inhibition of DCLK1 by Ruxolitinib.

Jang, D.M., Lim, H.J., Hahn, H., Lee, Y., Kim, H.K., Kim, H.S.

(2021) Int J Mol Sci 22

PubMed: 34445192 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms22168488
Primary Citation Related Structures:
7F3G

PubMed Abstract:
Given the functional attributes of Doublecortin-like kinase 1 (DCLK1) in tumor growth, invasion, metastasis, cell motility, and tumor stemness, it is emerging as a therapeutic target in gastrointestinal cancers. Although a series of specific or nonspecific ATP-competitive inhibitors were identified against DCLK1, different types of scaffolds that can be utilized for the development of highly selective inhibitors or structural understanding of binding specificities of the compounds remain limited. Here, we present our work to repurpose a Janus kinase 1 inhibitor, ruxolitinib as a DCLK1 inhibitor, showing micromolar binding affinity and inhibitory activity. Furthermore, to gain an insight into its interaction mode with DCLK1, a crystal structure of the ruxolitinib-complexed DCLK1 has been determined and analyzed. Ruxolitinib as a nonspecific DCLK1 inhibitor characterized in this work is anticipated to provide a starting point for the structure-guided discovery of selective DCLK1 inhibitors.

Organizational Affiliation

Research Institute, National Cancer Center, Goyang 10408, Gyeonggi, Korea.

Macromolecule Content

Total Structure Weight: 63.56 kDa
Atom Count: 4,331
Modeled Residue Count: 539
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 4 of Serine/threonine-protein kinase DCLK1	A, B	282	Homo sapiens	Mutation(s): 0 Gene Names: DCLK1, DCAMKL1, DCDC3A, KIAA0369 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15075 (Homo sapiens) Explore O15075 Go to UniProtKB: O15075
PHAROS: O15075 GTEx: ENSG00000133083
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15075
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RXT (Subject of Investigation/LOI) Query on RXT 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]	(3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile C₁₇ H₁₈ N₆ HFNKQEVNSGCOJV-OAHLLOKOSA-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
RXT	BindingDB: 7F3G	Kd: 68 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.210 (Depositor), 0.217 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.248	α = 90
b = 80.118	β = 90.662
c = 59.338	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Lim, H.J.

Jang, D.M.

Kim, H.S.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020R1C1C1009512

Revision History (Full details and data files)

Version 1.0: 2021-08-18
Type: Initial release
Version 1.1: 2022-04-27
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description