3IPY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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:  
    3IPX, 3IPY

  • 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 bioavailable inhibitor, compound 10 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine kinaseA, B241Homo sapiensMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B87
Query on B87

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], G [auth B], H [auth B]4-(1-benzothiophen-2-yl)-6-[4-(2-oxo-2-pyrrolidin-1-ylethyl)piperazin-1-yl]pyrimidine
C22 H25 N5 O S
NDLZMZLRTHDNSQ-UHFFFAOYSA-N
 Ligand Interaction
MLT
Query on MLT

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B87IC50 :  510   nM  PDBBind
B87IC50:  4000   nM  BindingDB
B87IC50:  510   nM  BindingDB
B87IC50:  510000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.556α = 90
b = 74.428β = 90
c = 239.097γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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