8PA6 | pdb_00008pa6

Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 2-aminoethenoadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

HINT1 Inhibitors as Selective Modulators of MOR-NMDAR Cross-Regulation and Non-Opioid Analgesia.

Dillenburg, M.Peterson, C.D.Dolot, R.Ligori, K.Kitto, K.F.Wilcox, G.L.Fairbanks, C.A.Wagner, C.R.

(2025) ACS Chem Neurosci 16: 604-618

  • DOI: https://doi.org/10.1021/acschemneuro.4c00564
  • Primary Citation of Related Structures:  
    8P8P, 8PA6, 8PA9, 8PAF, 8PAI

  • PubMed Abstract: 

    Human histidine triad nucleotide-binding protein 1 (HINT1) has recently become a protein of interest due to its involvement in several CNS processes, including neuroplasticity and the development of several neuropsychiatric disorders. Crucially, HINT1 behaves as a mediator for cross-regulation of the mu-opioid receptor (MOR) and N -methyl-d-aspartate receptor (NMDAR). Active site inhibition of HINT1 using small-molecule inhibitors has been demonstrated to have a significant impact on this cross-regulatory relationship in vivo. Herein, we describe the development of a series of ethenoadenosine HINT1 inhibitors to further evaluate the effect of HINT1 inhibition on morphine's blockade of NMDA-evoked behaviors, the development of acute endomorphin-2 tolerance, and analgesia. X-ray crystallographic analysis and HINT1 binding experiments demonstrate that modifications to the inhibitor nucleobase greatly impact the inhibitor binding interactions with HINT1. Our results reveal a complex structure-activity relationship for HINT1 inhibitors, in which minor modifications to the ethenoadenosine scaffold resulted in dramatic changes to their activity in these assays modeling MOR-NMDAR interaction. Specifically, we observed the ability of HINT1 inhibitors to selectively affect individual pathways of MOR-NMDAR crosstalk. Furthermore, we observed that a carbamate ethenoadenosine inhibitor of HINT1 can induce analgesia while not affecting opioid tolerance. Additionally, although past studies have indicated that the loss of HINT1 expression can result in the downregulation of p53, we have shown that the inhibition of HINT1 has no effect on either the expression of HINT1 or p53. These studies highlight the critical role of HINT1 in MOR-NMDAR crosstalk and demonstrate the intriguing potential of using HINT1 active-site inhibitors as tools to probe its role in these biochemical pathways and its potential as a novel pain target.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine triad nucleotide-binding protein 1
A, B
126Homo sapiensMutation(s): 0 
Gene Names: HINT1HINTPKCI1PRKCNH1
EC: 3 (PDB Primary Data), 3.4.22 (UniProt), 3.9.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49773 (Homo sapiens)
Explore P49773 
Go to UniProtKB:  P49773
PHAROS:  P49773
GTEx:  ENSG00000169567 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49773
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XKB (Subject of Investigation/LOI)
Query on XKB

Download Ideal Coordinates CCD File 
C [auth A]5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 2-aminoethenoadenosine
C23 H24 N8 O5
PHVKAGZMQNJNJY-QTQZEZTPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.845α = 90
b = 46.324β = 94.799
c = 63.971γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing

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 Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI146049

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection
  • Version 1.2: 2025-07-02
    Changes: Database references, Structure summary