9R1H | pdb_00009r1h

Inward-occluded structure of human glycine transporter 2 bound to substrate glycine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A reversible allosteric inhibitor of GlyT2 for neuropathic pain without on-target side effects.

Cantwell Chater, R.P.Peiser-Oliver, J.Pati, T.K.Quinn, A.S.Lotsaris, I.Frangos, Z.J.Anderson, K.E.Tischer, A.E.Williams-Noonan, B.J.Aubrey, K.R.O'Mara, M.L.Michaelides, M.Mohammadi, S.A.Cioffi, C.L.Vandenberg, R.J.Shahsavar, A.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-69616-5
  • Primary Citation of Related Structures:  
    9HUE, 9HUF, 9HUG, 9R1H

  • PubMed Abstract: 

    Chronic neuropathic pain, caused by nerve damage or disease, is increasing in prevalence, but current treatments are ineffective and over-reliant on opioids. The neuronal glycine transporter, GlyT2, regulates inhibitory glycinergic neurotransmission and represents a promising target for new analgesics. However, most GlyT2 inhibitors cause significant side effects, in part due to irreversible inhibition at analgesic doses. Here we develop a reversible inhibitor of GlyT2, RPI-GLYT2-82, and identify its binding site by determining cryo-EM structures of human GlyT2. We capture three fundamental conformational states of GlyT2 in the substrate-free state, and bound to either glycine, RPI-GLYT2-82 or the pseudo-irreversible inhibitor ORG25543. We demonstrate that RPI-GLYT2-82 dissociates from GlyT2 faster than ORG25543, providing analgesia in mouse neuropathic pain models without on-target side-effects or addiction liability. Our data provide a mechanistic understanding of allosteric inhibition of glycine transport, enabling structure-based design of non-opioid analgesics.


  • Organizational Affiliation
    • Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium- and chloride-dependent glycine transporter 2613Homo sapiensMutation(s): 0 
Gene Names: SLC6A5GLYT2NET1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y345 (Homo sapiens)
Explore Q9Y345 
Go to UniProtKB:  Q9Y345
PHAROS:  Q9Y345
GTEx:  ENSG00000165970 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y345
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:
RECONSTRUCTIONcryoSPARCv.4.5.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR368-2021-522
Novo Nordisk FoundationDenmarkNNF23OC0087107
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01DA048879

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release