Structure of PDB 2ymd Chain A Binding Site BS01

Receptor Information
>2ymd Chain A (length=212) Species: 6500 (Aplysia californica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDL
VYWEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYESTRPVQVL
SPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCALTFGSWVYSGF
EIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVV
KFRERRAGNGFF
Ligand information
Ligand IDSRO
InChIInChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2
InChIKeyQZAYGJVTTNCVMB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc2c(cc1O)c(c[nH]2)CCN
ACDLabs 10.04Oc1cc2c(cc1)ncc2CCN
CACTVS 3.341NCCc1c[nH]c2ccc(O)cc12
FormulaC10 H12 N2 O
NameSEROTONIN;
3-(2-AMINOETHYL)-1H-INDOL-5-OL
ChEMBLCHEMBL39
DrugBankDB08839
ZINCZINC000000057058
PDB chain2ymd Chain A Residue 1213 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ymd Structural Basis of Ligand Recognition in 5-Ht(3) Receptors.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		Y91 W145 V146 C188 C189 Y193
Binding residue
(residue number reindexed from 1)		Y91 W145 V146 C188 C189 Y193
Annotation score4
Binding affinityMOAD: Kd=693uM
PDBbind-CN: -logKd/Ki=3.16,Kd=693uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004888 transmembrane signaling receptor activity
GO:0005216 monoatomic ion channel activity
GO:0005230 extracellular ligand-gated monoatomic ion channel activity
GO:0005231 excitatory extracellular ligand-gated monoatomic ion channel activity
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:1904315 transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
Biological Process
GO:0006811 monoatomic ion transport
GO:0007165 signal transduction
GO:0007268 chemical synaptic transmission
GO:0034220 monoatomic ion transmembrane transport
GO:0042391 regulation of membrane potential
GO:0050877 nervous system process
GO:0060078 regulation of postsynaptic membrane potential
GO:0060079 excitatory postsynaptic potential
Cellular Component
GO:0016020 membrane
GO:0043005 neuron projection
GO:0045202 synapse
GO:0098794 postsynapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ymd, PDBe:2ymd, PDBj:2ymd
PDBsum2ymd
PubMed23196367
UniProtQ8WSF8

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