5MQT

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 

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 
• DOI: https://doi.org/10.1038/s41467-017-01582-5
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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), 2.7.1.76 (UniProt), 2.7.1.113 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens) Explore P27707  Go to UniProtKB:  P27707
PHAROS:  P27707

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	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
UDP	E [auth A], H [auth B], J [auth C], L [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
DCM	I [auth B], M [auth D]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 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.

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Funding Organization	Location	Grant Number
ARC	France	SL220130606659

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release