4Q1D

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 9 {2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-propyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine}


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.

Nomme, J.Li, Z.Gipson, R.M.Wang, J.Armijo, A.L.Le, T.Poddar, S.Smith, T.Santarsiero, B.D.Nguyen, H.A.Czernin, J.Alexandrova, A.N.Jung, M.E.Radu, C.G.Lavie, A.

(2014) J Med Chem 57: 9480-9494

  • DOI: 10.1021/jm501124j
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Recently, we have shown that small molecule dCK inhibitors in combination with pharmacological perturbations of de novo dNTP biosynthetic pathways could eliminate acute lymphoblastic leukemia cells in animal models. However, our previous lead compoun ...

    Recently, we have shown that small molecule dCK inhibitors in combination with pharmacological perturbations of de novo dNTP biosynthetic pathways could eliminate acute lymphoblastic leukemia cells in animal models. However, our previous lead compound had a short half-life in vivo. Therefore, we set out to develop dCK inhibitors with favorable pharmacokinetic properties. We delineated the sites of the inhibitor for modification, guided by crystal structures of dCK in complex with the lead compound and with derivatives. Crystal structure of the complex between dCK and the racemic mixture of our new lead compound indicated that the R-isomer is responsible for kinase inhibition. This was corroborated by kinetic analysis of the purified enantiomers, which showed that the R-isomer has >60-fold higher affinity than the S-isomer for dCK. This new lead compound has significantly improved metabolic stability, making it a prime candidate for dCK-inhibitor based therapies against hematological malignancies and, potentially, other cancers.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, and ‡Center for Pharmaceutical Biotechnology, University of Illinois at Chicago , Chicago, Illinois 60607, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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)
Find proteins for P27707 (Homo sapiens)
Explore P27707 
Go to UniProtKB:  P27707
NIH Common Fund Data Resources
PHAROS  P27707
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Y1
Query on 2Y1

Download CCD File 
A, B
(R)-2-((1-(2-(3-(2-fluoroethoxy)-4-methoxyphenyl)-5-propylthiazol-4-yl)ethyl)thio)pyrimidine-4,6-diamine
C21 H26 F N5 O2 S2
MGRJEGAUWXSZGM-GFCCVEGCSA-N
 Ligand Interaction
UDP
Query on UDP

Download CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2Y1IC50:  10   nM  BindingDB
2Y1IC50:  37   nM  BindingDB
2Y1Ki:  16.600000381469727   nM  Binding MOAD
2Y1Ki:  17   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.734α = 90
b = 68.734β = 90
c = 120.623γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-04-03 
  • Released Date: 2015-02-18 
  • Deposition Author(s): Nomme, J., Lavie, A.

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references