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 serotonin reuptake inhibition by a dual mode orthosteric/allosteric antidepressant

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

To be published.

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