9HCO | pdb_00009hco

Outward-open structure of human serotonin transporter bound to vilazodone

• PDB DOI: https://doi.org/10.2210/pdb9HCO/pdb
• EM Map EMD-52050: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Homo sapiens, Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-11-11 Released: 2025-09-17 
• Deposition Author(s): Kalenderoglou, I.E., Tillmann, P., Loland, C.J.
• Funding Organization(s): Novo Nordisk Foundation, Independent Research Fund Denmark - Medical Sciences, H2020 Marie Curie Actions of the European Commission, The Carlsberg Foundation, National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of vilazodone dual binding mode to the serotonin transporter.

Kalenderoglou, I.E., Nygaard, A., Vogt, C.D., Turaev, A., Pape, T., Adams, N.B.P., Newman, A.H., Loland, C.J.

(2025) Nat Commun 16: 10119-10119

• PubMed: 41253806 
• DOI: https://doi.org/10.1038/s41467-025-65202-3
• Primary Citation Related Structures: 
  9HCO


• PubMed Abstract: 
  

  The serotonin transporter (SERT) plays a pivotal role in regulating serotonin (5-HT) signaling and is a key target in the treatment of psychiatric disorders. SERT has a binding site (S1) for 5-HT that also serves as a high-affinity binding site for antidepressants. The antidepressant vilazodone has been shown to inhibit SERT by binding to an allosteric site. Here, we present the cryo-EM structure of SERT with vilazodone bound to the S1 site and extending towards the allosteric site. We systematically dissect the vilazodone molecule into fragments and find that the terminal indole ring is the key determinant of its high affinity to SERT. Further, unlike typical Na ⁺ -dependent SERT-selective antidepressants, vilazodone exhibits a dissociation constant (K _D ) for purified SERT in the nanomolar range both in the presence and absence of Na ⁺ . We substantiate this binding mode by exploring the conformational impact of vilazodone binding to SERT using site-specific insertion of the fluorescent non-canonical amino acid Anap. Our results offer molecular insight into the distinct pharmacological profile of a clinically used polymodal antidepressant.

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Organizational Affiliation: 
• Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, US.
NanoTemper Technologies, Floessegasse 4, Munich, Germany.
Structural Molecular Biology Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 124.71 kDa 
• Atom Count: 6,107 
• Modeled Residue Count: 769 
• Deposited Residue Count: 1,130 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent serotonin transporter	A	685	Homo sapiens	Mutation(s): 0  Gene Names: SLC6A4, HTT, SERT Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P31645 (Homo sapiens) Explore P31645  Go to UniProtKB:  P31645
PHAROS:  P31645 GTEx:  ENSG00000108576

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
15B8 Fab heavy chain	B [auth H]	229	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
15B8 Fab light chain	C [auth L]	216	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YG7 (Subject of Investigation/LOI)	D [auth A]	5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide C26 H27 N5 O2 SGEGOXDYSFKCPT-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Kalenderoglou, I.E., Tillmann, P., Loland, C.J.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF22OC0079091
Independent Research Fund Denmark - Medical Sciences	Denmark	1030-00036B
H2020 Marie Curie Actions of the European Commission	European Union	860954
The Carlsberg Foundation	Denmark	1030-00036B
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	Z1A DA000389
Novo Nordisk Foundation	Denmark	NNF17SA0024386
Novo Nordisk Foundation	Denmark	NNF22OC0075808

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 1.1: 2026-05-20
  Changes: Data collection, Database references