5MQT | pdb_00005mqt

Crystal structure of dCK mutant C3S in complex with imatinib and UDP

PDB DOI: https://doi.org/10.2210/pdb5MQT/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-12-20 Released: 2017-11-22
Deposition Author(s): Saez-Ayala, M., Rebuffet, E., Hammam, K., Gros, L., Lopez, S., Hajem, B., Humbert, M., Baudelet, E., Audebert, S., Betzi, S., Lugari, A., Combes, S., Pez, D., Letard, S., Mansfield, C., Moussy, A., de Sepulveda, P., Morelli, X., Dubreuil, P.
Funding Organization(s): ARC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.254 (Depositor), 0.237 (DCC)
R-Value Work:
0.186 (Depositor)
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

Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology.

Hammam, K., Saez-Ayala, M., Rebuffet, E., Gros, L., Lopez, S., Hajem, B., Humbert, M., Baudelet, E., Audebert, S., Betzi, S., Lugari, A., Combes, S., Letard, S., Casteran, N., Mansfield, C., Moussy, A., De Sepulveda, P., Morelli, X., Dubreuil, P.

(2017) Nat Commun 8: 1420-1420

PubMed: 29127277 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-017-01582-5
Primary Citation Related Structures:
5MQJ, 5MQL, 5MQT

PubMed Abstract:
Masitinib, a highly selective protein kinase inhibitor, can sensitise gemcitabine-refractory cancer cell lines when used in combination with gemcitabine. Here we report a reverse proteomic approach that identifies the target responsible for this sensitisation: the deoxycytidine kinase (dCK). Masitinib, as well as other protein kinase inhibitors, such as imatinib, interact with dCK and provoke an unforeseen conformational-dependent activation of this nucleoside kinase, modulating phosphorylation of nucleoside analogue drugs. This phenomenon leads to an increase of prodrug phosphorylation of most of the chemotherapeutic drugs activated by this nucleoside kinase. The unforeseen dual activity of protein kinase inhibition/nucleoside kinase activation could be of great therapeutic benefit, through either reducing toxicity of therapeutic agents by maintaining effectiveness at lower doses or by counteracting drug resistance initiated via down modulation of dCK target.

Organizational Affiliation

Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM, CNRS, Aix-Marseille Univ, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, 13009, France.

Macromolecule Content

Total Structure Weight: 139.34 kDa
Atom Count: 7,588
Modeled Residue Count: 915
Deposited Residue Count: 1,156
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxycytidine kinase	A, B, C, D	289	Homo sapiens	Mutation(s): 3 Gene Names: DCK EC: 2.7.1.74 (PDB Primary Data), 2.7.1.113 (UniProt), 2.7.1.76 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens) Explore P27707 Go to UniProtKB: P27707
PHAROS: P27707 GTEx: ENSG00000156136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27707
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STI Query on STI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C₂₉ H₃₁ N₇ O KTUFNOKKBVMGRW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C], L [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
DCM Query on DCM Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth D] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] mmCIF format, chain I [auth B] mmCIF format, chain M [auth D]	I [auth B], M [auth D]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₇ P NCMVOABPESMRCP-SHYZEUOFSA-N		Interactions Focus chain I [auth B] Focus chain M [auth D] Interactions & Density Focus chain I [auth B] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.254 (Depositor), 0.237 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.190 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.3	α = 90
b = 93.3	β = 90
c = 342.715	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Funding Organization	Location	Grant Number
ARC	France	SL220130606659

Revision History (Full details and data files)

Version 1.0: 2017-11-22
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary