4PD6

Crystal structure of vcCNT-7C8C bound to uridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters.

Johnson, Z.L.Lee, J.H.Lee, K.Lee, M.Kwon, D.Y.Hong, J.Lee, S.Y.

(2014) Elife 3: e03604-e03604

  • DOI: 10.7554/eLife.03604
  • Primary Citation of Related Structures:  
    4PB1, 4PB2, 4PDA, 4PD8, 4PD9, 4PD5, 4PD6, 4PD7

  • PubMed Abstract: 
  • Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents ...

    Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, United States sylee@biochem.duke.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NupC family proteinA424Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 2 
Gene Names: VC_2352
Find proteins for Q9KPL5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KPL5 
Go to UniProtKB:  Q9KPL5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download Ideal Coordinates CCD File 
D [auth A]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
URI
Query on URI

Download Ideal Coordinates CCD File 
B [auth A]URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
URIKd:  36000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.65α = 90
b = 119.65β = 90
c = 83.11γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM100984

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence