7ZI8 | pdb_00007zi8

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0602 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.263 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZI8

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 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.

Macromolecule Content 

  • Total Structure Weight: 33.67 kDa 
  • Atom Count: 2,018 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 280 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J5U
(Subject of Investigation/LOI)

Query on J5U



Download:Ideal Coordinates CCD File
C [auth A]2-[2-[[2-methyl-5-[6-[2-(4-methylpiperazin-1-yl)ethyl]pyridin-3-yl]phenyl]-propyl-amino]-1,3-thiazol-4-yl]pyrimidine-4,6-diamine
C29 H37 N9 S
YNFSLZUCOOMOSV-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: 1.99 Å
  • R-Value Free:  0.263 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.618α = 90
b = 68.618β = 90
c = 121.247γ = 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