3IPX

X-Ray structure of Human Deoxycytidine Kinase in complex with ADP and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors.

Jessop, T.C.Tarver, J.E.Carlsen, M.Xu, A.Healy, J.P.Heim-Riether, A.Fu, Q.Taylor, J.A.Augeri, D.J.Shen, M.Stouch, T.R.Swanson, R.V.Tari, L.W.Hunter, M.Hoffman, I.Keyes, P.E.Yu, X.C.Miranda, M.Liu, Q.Swaffield, J.C.David Kimball, S.Nouraldeen, A.Wilson, A.G.Foushee, A.M.Jhaver, K.Finch, R.Anderson, S.Oravecz, T.Carson, K.G.

(2009) Bioorg.Med.Chem.Lett. 19: 6784-6787

  • DOI: 10.1016/j.bmcl.2009.09.081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of deoxycytidine kinase inhibitors was simultaneously optimized for potency and PK properties. A co-crystal structure then allowed merging this series with a high throughput screening hit to afford a highly potent, selective and orally bioav ...

    A series of deoxycytidine kinase inhibitors was simultaneously optimized for potency and PK properties. A co-crystal structure then allowed merging this series with a high throughput screening hit to afford a highly potent, selective and orally bioavailable inhibitor, compound 10. This compound showed dose dependent inhibition of deoxycytidine kinase in vivo.


    Organizational Affiliation

    Lexicon Pharmaceuticals, Princeton, NJ 08540, United States. tjessop@lexpharma.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine kinase
A
241Homo sapiensGene Names: DCK
EC: 2.7.1.74
Find proteins for P27707 (Homo sapiens)
Go to Gene View: DCK
Go to UniProtKB:  P27707
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
B86
Query on B86

Download SDF File 
Download CCD File 
A
2'-deoxy-5-fluorocytidine
C9 H12 F N3 O4
IDYKCXHJJGMAEV-RRKCRQDMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B86IC50: >4000 - 120000 nM (100) BINDINGDB
B86IC50: 120 nM BINDINGMOAD
B86IC50: 120 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.238α = 90.00
b = 80.238β = 90.00
c = 93.950γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance