ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:SLC6A4

Protein Summary

Gene summary

Gene name: SLC6A4
ASpdb.0 ID: 6532
	Gene
Gene symbol	SLC6A4
Gene ID	6532
Gene name	solute carrier family 6 member 4
Synonyms	5-HTT\|5-HTTLPR\|5HTT\|HTT\|OCD1\|SERT\|SERT1\|hSERT
Cytomap	17q11.2
Type of gene	protein-coding
Description	sodium-dependent serotonin transporter5-hydroxytryptamine (serotonin) transporter5HT transporterNa+/Cl- dependent serotonin transporterserotonin transporter 1solute carrier family 6 (neurotransmitter transporter), member 4solute carrier family 6 (ne
Modification date	20240411
UniProtAcc	P31645

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	SLC6A4	GO:0005178	integrin binding	18317590
Gene	SLC6A4	GO:0005335	serotonin:sodium:chloride symporter activity	8987735\|10407194\|17506858
Gene	SLC6A4	GO:0005886	plasma membrane	12869649\|16870614\|17506858\|18317590
Gene	SLC6A4	GO:0008504	monoamine transmembrane transporter activity	16024787
Gene	SLC6A4	GO:0009636	response to toxic substance	17575980
Gene	SLC6A4	GO:0012505	endomembrane system	17506858
Gene	SLC6A4	GO:0015297	antiporter activity	27756841
Gene	SLC6A4	GO:0015844	monoamine transport	16024787
Gene	SLC6A4	GO:0031402	sodium ion binding	34851672
Gene	SLC6A4	GO:0045121	membrane raft	16870614
Gene	SLC6A4	GO:0051378	serotonin binding	34851672
Gene	SLC6A4	GO:0051610	serotonin uptake	8987735\|16870614\|17506858\|18317590\|21730057\|27756841

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
P31645-1	P31645-1_6awo_A.pdb	6AWO	X-ray	3.53	A	76	617

ASpdb's canonical and alternatively spliced isoform information.

accession_id

gene_name

canonical_id

alternative_id

canonical_length

alternative_length

canonical_start

canonical_end

type

originalSEQ

variationSEQ

alternative_start

alternative_end

P31645

SLC6A4

P31645-1

P31645-2

630

672

Substitution

MSQSRRVNPDDRELGGDLQIQAPRDQLGSLADGHQCHLLTSRM

Multiple sequence alignment of our canonical and alternatively spliced SLC6A4

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SLC6A4

UniProt-id	ENSG	ENST	ENSP
P31645-1	ENSG00000108576.10	ENST00000261707.7	ENSP00000261707.3
P31645-1	ENSG00000108576.10	ENST00000401766.6	ENSP00000385822.2
P31645-1	ENSG00000108576.10	ENST00000650711.1	ENSP00000498537.1

UniProt-id	NM ID	NP ID
P31645-1	NM_001045.5	NP_001036.1

Amino acid sequences of our canonical and alternatively spliced SLC6A4

accession_id	Protein sequence
P31645-1	METTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYSAVPSPGAGDDTRHSIPATTTTLVAELHQGERETWGKKVDFLL SVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIM AWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSI WKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQD ALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDSTFAGLEGVITAV LDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRIC WVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETPTEIPCGDIRLNAV
P31645-2	MSQSRRVNPDDRELGGDLQIQAPRDQLGSLADGHQCHLLTSRMETTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYS AVPSPGAGDDTRHSIPATTTTLVAELHQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELA LGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPA EEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQ KLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFI TYAEAIANMPASTFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATG PAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFIC

Protein Functional Features

Main function of this protein. (from UniProt)

SLC6A4 (go to UniProt):P31645

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
P31645	Topological domain	1	87	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305	Type=Substitution;Start=1;End=1
P31645	Region	1	59	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1
P31645	Compositional bias	1	15	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1

Gene Isoform Structures and Expression Levels for SLC6A4

Gene structures of our canonical and alternative spliced genes of SLC6A4
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of P31645-1

3D view using mol* of P31645-2

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of P31645-1

pLDDT distribution across the protein length of P31645-2

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of P31645-1

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
P31645-1	1.037	387	1.039	1150.765	0.583	0.754	0.904	0.586	1.083	0.541	1.025	95,96,98,99,100,103,104,107,108,169,172,173,175,17 6,179,182,206,212,220,225,226,229,230,232,233,234, 237,239,324,327,328,331,332,335,336,338,341,343,38 6,390,392,396,397,399,400,401,402,403,404,408,409, 412,438,439,442,443,486,489,490,493,494,495,497,49 8,499,555,556,559,560,561,562,563,564,565,566,567, 568,569,570,575
P31645-2	1.139	217	1.104	556.003	0.365	0.905	1.119	0.978	1.162	0.841	1.281	137,138,140,141,142,143,145,146,147,149,150,153,15 4,163,211,214,215,217,218,221,373,374,375,377,378, 380,383,443,444,445,448,449,473,480,481,484,485,53 1,532,535,536,539,540,543,598

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of P31645-1_P31645-1_6awo_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P31645-1_6awo_A_P31645-2.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P31645-1_P31645-2.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/P31645-1_vs_P31645-2.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/P31645-1_vs_P31645-2.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to SLC6A4

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P31645	SLC6A4	DB04821	Nomifensine	approved, withdrawn
P31645	SLC6A4	DB01242	Clomipramine	approved, investigational, vet_approved	inhibitor
P31645	SLC6A4	DB00193	Tramadol	approved, investigational	inhibitor
P31645	SLC6A4	DB04832	Zimelidine	approved, withdrawn
P31645	SLC6A4	DB06204	Tapentadol	approved	inhibitor
P31645	SLC6A4	DB00514	Dextromethorphan	approved	inhibitor
P31645	SLC6A4	DB01238	Aripiprazole	approved, investigational	modulator
P31645	SLC6A4	DB12305	Dasotraline	investigational
P31645	SLC6A4	DB01151	Desipramine	approved, investigational	inhibitor
P31645	SLC6A4	DB01149	Nefazodone	approved, withdrawn	inhibitor
P31645	SLC6A4	DB04836	Amineptine	illicit, withdrawn
P31645	SLC6A4	DB00543	Amoxapine	approved	inhibitor
P31645	SLC6A4	DB08918	Levomilnacipran	approved, investigational	inhibitor
P31645	SLC6A4	DB00408	Loxapine	approved	binder
P31645	SLC6A4	DB06156	Tesofensine	investigational
P31645	SLC6A4	DB00540	Nortriptyline	approved	inhibitor
P31645	SLC6A4	DB01191	Dexfenfluramine	approved, illicit, investigational, withdrawn	inhibitor
P31645	SLC6A4	DB01175	Escitalopram	approved	inhibitor
P31645	SLC6A4	DB00574	Fenfluramine	approved, illicit, investigational, withdrawn	substrate, inhibitor
P31645	SLC6A4	DB06700	Desvenlafaxine	approved, investigational	inhibitor
P31645	SLC6A4	DB06148	Mianserin	approved, investigational	inhibitor
P31645	SLC6A4	DB00988	Dopamine	approved	inhibitor
P31645	SLC6A4	DB09195	Lorpiprazole	approved	antagonist
P31645	SLC6A4	DB09186	Nisoxetine	experimental
P31645	SLC6A4	DB09167	Dosulepin	approved	inhibitor
P31645	SLC6A4	DB00182	Amphetamine	approved, illicit, investigational	binder
P31645	SLC6A4	DB09068	Vortioxetine	approved, investigational	inhibitor
P31645	SLC6A4	DB00924	Cyclobenzaprine	approved	inhibitor
P31645	SLC6A4	DB00289	Atomoxetine	approved	binder
P31645	SLC6A4	DB05688	CRx-119	investigational
P31645	SLC6A4	DB00715	Paroxetine	approved, investigational	inhibitor
P31645	SLC6A4	DB00656	Trazodone	approved, investigational	inhibitor
P31645	SLC6A4	DB00579	Mazindol	approved, investigational	inhibitor
P31645	SLC6A4	DB00454	Meperidine	approved	binder
P31645	SLC6A4	DB00472	Fluoxetine	approved, vet_approved	inhibitor
P31645	SLC6A4	DB00852	Pseudoephedrine	approved	inhibitor
P31645	SLC6A4	DB00661	Verapamil	approved	unknown
P31645	SLC6A4	DB00215	Citalopram	approved	inhibitor
P31645	SLC6A4	DB00907	Cocaine	approved, illicit	inhibitor
P31645	SLC6A4	DB00245	Benzatropine	approved	inhibitor
P31645	SLC6A4	DB06684	Vilazodone	approved	inhibitor
P31645	SLC6A4	DB08839	Serotonin	investigational, nutraceutical
P31645	SLC6A4	DB00476	Duloxetine	approved	inhibitor
P31645	SLC6A4	DB05422	OPC-14523	investigational
P31645	SLC6A4	DB00285	Venlafaxine	approved	inhibitor
P31645	SLC6A4	DB00458	Imipramine	approved	inhibitor
P31645	SLC6A4	DB00191	Phentermine	approved, illicit	inhibitor
P31645	SLC6A4	DB00726	Trimipramine	approved	inhibitor
P31645	SLC6A4	DB09225	Zotepine	approved, investigational, withdrawn	antagonist
P31645	SLC6A4	DB00321	Amitriptyline	approved	inhibitor
P31645	SLC6A4	DB09016	Butriptyline	approved, withdrawn	antagonist, inhibitor
P31645	SLC6A4	DB01142	Doxepin	approved, investigational	inhibitor
P31645	SLC6A4	DB01363	Ephedra sinica root	nutraceutical	negative modulator
P31645	SLC6A4	DB01114	Chlorpheniramine	approved	inhibitor
P31645	SLC6A4	DB00344	Protriptyline	approved	inhibitor
P31645	SLC6A4	DB01105	Sibutramine	approved, illicit, investigational, withdrawn	inhibitor
P31645	SLC6A4	DB00176	Fluvoxamine	approved, investigational	inhibitor
P31645	SLC6A4	DB01104	Sertraline	approved	inhibitor, binder, downregulator
P31645	SLC6A4	DB04889	Bicifadine	investigational
P31645	SLC6A4	DB01577	Metamfetamine	approved, illicit, withdrawn	negative modulator
P31645	SLC6A4	DB01442	MMDA	experimental, illicit	negative modulator
P31645	SLC6A4	DB04896	Milnacipran	approved, investigational	inhibitor
P31645	SLC6A4	DB01454	Midomafetamine	experimental, illicit, investigational	negative modulator
P31645	SLC6A4	DB05964	Amitifadine	investigational
P31645	SLC6A4	DB06077	Lumateperone	approved, investigational	inhibitor
P31645	SLC6A4	DB06701	Dexmethylphenidate	approved, investigational	inhibitor
P31645	SLC6A4	DB00805	Minaprine	approved	inhibitor
P31645	SLC6A4	DB01472	4-Methoxyamphetamine	experimental, illicit	inhibitor

Related Diseases to SLC6A4

Previous studies relating to the alternative splicing of SLC6A4 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in SLC6A4

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance