7ZIB

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0635 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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

From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.

Saez-Ayala, M.Hoffer, L.Abel, S.Ben Yaala, K.Sicard, B.Andrieu, G.P.Latiri, M.Davison, E.K.Ciufolini, M.A.Bremond, P.Rebuffet, E.Roche, P.Derviaux, C.Voisset, E.Montersino, C.Castellano, R.Collette, Y.Asnafi, V.Betzi, S.Dubreuil, P.Combes, S.Morelli, X.

(2023) Nat Commun 14: 3079-3079

  • DOI: https://doi.org/10.1038/s41467-023-38668-2
  • Primary Citation of Related Structures:  
    7ZI1, 7ZI2, 7ZI3, 7ZI5, 7ZI6, 7ZI7, 7ZI8, 7ZI9, 7ZIA, 7ZIB

  • PubMed Abstract: 

    Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy.


  • Organizational Affiliation

    Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France. magali.saez-ayala@inserm.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxycytidine kinase280Homo sapiensMutation(s): 5 
Gene Names: DCK
EC: 2.7.1.74 (PDB Primary Data), 2.7.1.76 (PDB Primary Data), 2.7.1.113 (PDB Primary Data)
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27707
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J7I (Subject of Investigation/LOI)
Query on J7I

Download Ideal Coordinates CCD File 
C [auth A]2-[2-[[5-[3-methoxy-4-(4-methylpiperazin-1-yl)sulfonyl-phenyl]-2-methyl-phenyl]-propyl-amino]-1,3-thiazol-4-yl]pyrimidine-4,6-diamine
C29 H36 N8 O3 S2
VYVDDCIZEXCGHT-UHFFFAOYSA-N
UDP
Query on UDP

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.506α = 90
b = 68.506β = 90
c = 120.334γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondation ARCFranceSL220130606659

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description