3IPX

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine kinase241Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27707
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
B86
Query on B86
Download Ideal Coordinates CCD File 
C [auth A]2'-deoxy-5-fluorocytidine
C9 H12 F N3 O4
IDYKCXHJJGMAEV-RRKCRQDMSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B86 BindingDB:  3IPX IC50: min: 4000, max: 1.20e+5 (nM) from 2 assay(s)
PDBBind:  3IPX IC50: 120 (nM) from 1 assay(s)
Binding MOAD:  3IPX IC50: 120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.238α = 90
b = 80.238β = 90
c = 93.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description