Structure of PDB 6vrl Chain A Binding Site BS01

Receptor Information
>6vrl Chain A (length=541) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAI
FGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYY
NTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTS
PAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKT
SGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVW
IDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSG
FVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAII
FFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFG
SLVTLTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVK
EMLGFSPGWFWRICWVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSII
LGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP
Ligand information
Ligand IDRFY
InChIInChI=1S/C19H20INO3/c20-15-3-1-13(2-4-15)17-7-8-21-10-14(17)11-22-16-5-6-18-19(9-16)24-12-23-18/h1-6,9,14,17,21H,7-8,10-12H2/t14-,17-/m0/s1
InChIKeyQJFNUDYGOMCKMV-YOEHRIQHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c4(ccc(C1CCNCC1COc2cc3c(cc2)OCO3)cc4)I
CACTVS 3.385Ic1ccc(cc1)[C@@H]2CCNC[C@H]2COc3ccc4OCOc4c3
OpenEye OEToolkits 2.0.7c1cc(ccc1C2CCNCC2COc3ccc4c(c3)OCO4)I
CACTVS 3.385Ic1ccc(cc1)[CH]2CCNC[CH]2COc3ccc4OCOc4c3
OpenEye OEToolkits 2.0.7c1cc(ccc1[C@@H]2CCNC[C@H]2COc3ccc4c(c3)OCO4)I
FormulaC19 H20 I N O3
NameI-paroxetine;
(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}-4-(4-iodophenyl)piperidine
ChEMBL
DrugBank
ZINC
PDB chain6vrl Chain A Residue 704 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6vrl Chemical and structural investigation of the paroxetine-human serotonin transporter complex.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		Y95 A96 D98 I172 F335 F341 S438 T439 G442 L443 T497 V501
Binding residue
(residue number reindexed from 1)		Y19 A20 D22 I96 F259 F265 S362 T363 G366 L367 T421 V425
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005178 integrin binding
GO:0005261 monoatomic cation channel activity
GO:0005326 neurotransmitter transmembrane transporter activity
GO:0005335 serotonin:sodium:chloride symporter activity
GO:0005515 protein binding
GO:0008504 monoamine transmembrane transporter activity
GO:0015297 antiporter activity
GO:0017075 syntaxin-1 binding
GO:0019811 cocaine binding
GO:0031402 sodium ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0050998 nitric-oxide synthase binding
GO:0051015 actin filament binding
GO:0051378 serotonin binding
Biological Process
GO:0001666 response to hypoxia
GO:0006836 neurotransmitter transport
GO:0006837 serotonin transport
GO:0006865 amino acid transport
GO:0007584 response to nutrient
GO:0007613 memory
GO:0007623 circadian rhythm
GO:0009410 response to xenobiotic stimulus
GO:0009636 response to toxic substance
GO:0010628 positive regulation of gene expression
GO:0014064 positive regulation of serotonin secretion
GO:0015844 monoamine transport
GO:0021941 negative regulation of cerebellar granule cell precursor proliferation
GO:0032227 negative regulation of synaptic transmission, dopaminergic
GO:0032355 response to estradiol
GO:0035725 sodium ion transmembrane transport
GO:0042310 vasoconstriction
GO:0042713 sperm ejaculation
GO:0045665 negative regulation of neuron differentiation
GO:0045787 positive regulation of cell cycle
GO:0046621 negative regulation of organ growth
GO:0048148 behavioral response to cocaine
GO:0048484 enteric nervous system development
GO:0048854 brain morphogenesis
GO:0051610 serotonin uptake
GO:0051899 membrane depolarization
GO:0070527 platelet aggregation
GO:0071300 cellular response to retinoic acid
GO:0071321 cellular response to cGMP
GO:0090067 regulation of thalamus size
GO:0098810 neurotransmitter reuptake
GO:1990708 conditioned place preference
Cellular Component
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0010008 endosome membrane
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0042734 presynaptic membrane
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0045121 membrane raft
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0070161 anchoring junction
GO:0099154 serotonergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vrl, PDBe:6vrl, PDBj:6vrl
PDBsum6vrl
PubMed32618269
UniProtP31645|SC6A4_HUMAN Sodium-dependent serotonin transporter (Gene Name=SLC6A4)

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