8TZI | pdb_00008tzi

Human equilibrative nucleoside transporter-1, JH-ENT-01 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.256 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8TZI

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Design of an equilibrative nucleoside transporter subtype 1 inhibitor for pain relief.

Wright, N.J.Matsuoka, Y.Park, H.He, W.Webster, C.G.Furutani, K.Fedor, J.G.McGinnis, A.Zhao, Y.Chen, O.Bang, S.Fan, P.Spasojevic, I.Hong, J.Ji, R.R.Lee, S.Y.

(2024) Nat Commun 15: 10738-10738

  • DOI: https://doi.org/10.1038/s41467-024-54914-7
  • Primary Citation Related Structures: 
    8TZI

  • PubMed Abstract: 

    The current opioid crisis urgently calls for developing non-addictive pain medications. Progress has been slow, highlighting the need to uncover targets with unique mechanisms of action. Extracellular adenosine alleviates pain by activating the adenosine A1 receptor (A1R). However, efforts to develop A1R agonists have faced obstacles. The equilibrative nucleoside transporter subtype 1 (ENT1) plays a crucial role in regulating adenosine levels across cell membranes. We postulate that ENT1 inhibition may enhance extracellular adenosine levels, potentiating endogenous adenosine action at A1R and leading to analgesic effects. Here, we modify the ENT1 inhibitor dilazep based on its complex X-ray structure and show that this modified inhibitor reduces neuropathic and inflammatory pain in animal models while dilazep does not. Notably, our ENT1 inhibitor surpasses gabapentin in analgesic efficacy in a neuropathic pain model. Additionally, our inhibitor exhibits less cardiac side effect than dilazep via systemic administration and shows no side effects via local/intrathecal administration. ENT1 is colocalized with A1R in mouse and human dorsal root ganglia, and the analgesic effect of our inhibitor is linked to A1R. Our studies reveal ENT1 as a therapeutic target for analgesia, highlighting the promise of rationally designed ENT1 inhibitors for non-opioid pain medications.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.

Macromolecule Content 

  • Total Structure Weight: 51.73 kDa 
  • Atom Count: 3,110 
  • Modeled Residue Count: 385 
  • Deposited Residue Count: 442 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Equilibrative nucleoside transporter 1442Homo sapiensMutation(s): 3 
Gene Names: SLC29A1ENT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99808 (Homo sapiens)
Explore Q99808 
Go to UniProtKB:  Q99808
PHAROS:  Q99808
GTEx:  ENSG00000112759 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99808
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U00
(Subject of Investigation/LOI)

Query on U00



Download:Ideal Coordinates CCD File
H [auth A]3-(4-{3-[(3,4,5-trimethoxybenzoyl)oxy]propyl}-1,4-diazepan-1-yl)propyl 3,4-dimethoxy-5-[(4-nitrophenyl)methoxy]benzoate
C37 H47 N3 O12
FYJNHJQOMBDFFA-UHFFFAOYSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.413α = 90
b = 72.413β = 90
c = 173.92γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137421

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Database references, Structure summary
  • Version 2.0: 2026-04-15
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary