4KCG

Human dCK C4S-S74E mutant in complex with UDP and the DI-39 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication.

Nathanson, D.A.Armijo, A.L.Tom, M.Li, Z.Dimitrova, E.Austin, W.R.Nomme, J.Campbell, D.O.Ta, L.Le, T.M.Lee, J.T.Darvish, R.Gordin, A.Wei, L.Liao, H.I.Wilks, M.Martin, C.Sadeghi, S.Murphy, J.M.Boulos, N.Phelps, M.E.Faull, K.F.Herschman, H.R.Jung, M.E.Czernin, J.Lavie, A.Radu, C.G.

(2014) J Exp Med 211: 473-486

  • DOI: 10.1084/jem.20131738
  • Primary Citation of Related Structures:  
    4KCG

  • PubMed Abstract: 
  • Pharmacological targeting of metabolic processes in cancer must overcome redundancy in biosynthetic pathways. Deoxycytidine (dC) triphosphate (dCTP) can be produced both by the de novo pathway (DNP) and by the nucleoside salvage pathway (NSP). However, the role of the NSP in dCTP production and DNA synthesis in cancer cells is currently not well understood ...

    Pharmacological targeting of metabolic processes in cancer must overcome redundancy in biosynthetic pathways. Deoxycytidine (dC) triphosphate (dCTP) can be produced both by the de novo pathway (DNP) and by the nucleoside salvage pathway (NSP). However, the role of the NSP in dCTP production and DNA synthesis in cancer cells is currently not well understood. We show that acute lymphoblastic leukemia (ALL) cells avoid lethal replication stress after thymidine (dT)-induced inhibition of DNP dCTP synthesis by switching to NSP-mediated dCTP production. The metabolic switch in dCTP production triggered by DNP inhibition is accompanied by NSP up-regulation and can be prevented using DI-39, a new high-affinity small-molecule inhibitor of the NSP rate-limiting enzyme dC kinase (dCK). Positron emission tomography (PET) imaging was useful for following both the duration and degree of dCK inhibition by DI-39 treatment in vivo, thus providing a companion pharmacodynamic biomarker. Pharmacological co-targeting of the DNP with dT and the NSP with DI-39 was efficacious against ALL models in mice, without detectable host toxicity. These findings advance our understanding of nucleotide metabolism in leukemic cells, and identify dCTP biosynthesis as a potential new therapeutic target for metabolic interventions in ALL and possibly other hematological malignancies.


    Organizational Affiliation

    Department of Molecular and Medical Pharmacology; 2 Ahmanson Translational Imaging Division; 3 Department of Biomathematics; 4 The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and the Semel Institute for Neuroscience and Human Behavior; 5 Department of Biological Chemistry; and 6 Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine kinaseA, B280Homo sapiensMutation(s): 5 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27707
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1QC
Query on 1QC

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
N-{2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide
C21 H28 N6 O4 S3
VWMTUHOSEYDVPP-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1QC BindingDB:  4KCG Ki: 0.5 (nM) from 1 assay(s)
IC50: min: 4.9, max: 14 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.731α = 90
b = 68.731β = 90
c = 120.588γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references