Structure of PDB 7ynm Chain I Binding Site BS01

Receptor Information
>7ynm Chain I (length=61) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAG
SIAAATGFVKK
Ligand information
Ligand IDTFX
InChIInChI=1S/C17H19N2S/c1-12-5-10-15-16(11-12)20-17(19(15)4)13-6-8-14(9-7-13)18(2)3/h5-11H,1-4H3/q+1
InChIKeyFXEKRIDRIFBJOR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN(C)c1ccc(cc1)c2sc3cc(C)ccc3[n+]2C
OpenEye OEToolkits 1.7.0Cc1ccc2c(c1)sc([n+]2C)c3ccc(cc3)N(C)C
ACDLabs 12.01s2c1cc(ccc1[n+](c2c3ccc(N(C)C)cc3)C)C
FormulaC17 H19 N2 S
Name2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium;
Thioflavin T
ChEMBLCHEMBL57267
DrugBank
ZINCZINC000003861628
PDB chain7ynm Chain G Residue 201 [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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PDB7ynm ThT-bound alpha-synuclein fibrils conformation 1
Resolution2.9 Å
Binding residue
(original residue number in PDB)		Y39 K80
Binding residue
(residue number reindexed from 1)		Y3 K44
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000149 SNARE binding
GO:0000287 magnesium ion binding
GO:0000976 transcription cis-regulatory region binding
GO:0003779 actin binding
GO:0004860 protein kinase inhibitor activity
GO:0005504 fatty acid binding
GO:0005507 copper ion binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0008198 ferrous iron binding
GO:0008270 zinc ion binding
GO:0008289 lipid binding
GO:0016491 oxidoreductase activity
GO:0019894 kinesin binding
GO:0030544 Hsp70 protein binding
GO:0042393 histone binding
GO:0042802 identical protein binding
GO:0043014 alpha-tubulin binding
GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0046872 metal ion binding
GO:0048156 tau protein binding
GO:0051219 phosphoprotein binding
GO:0060090 molecular adaptor activity
GO:0060961 phospholipase D inhibitor activity
GO:0070840 dynein complex binding
GO:1903136 cuprous ion binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001774 microglial cell activation
GO:0001921 positive regulation of receptor recycling
GO:0001956 positive regulation of neurotransmitter secretion
GO:0001963 synaptic transmission, dopaminergic
GO:0006469 negative regulation of protein kinase activity
GO:0006631 fatty acid metabolic process
GO:0006638 neutral lipid metabolic process
GO:0006644 phospholipid metabolic process
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007006 mitochondrial membrane organization
GO:0007268 chemical synaptic transmission
GO:0007269 neurotransmitter secretion
GO:0008344 adult locomotory behavior
GO:0009410 response to xenobiotic stimulus
GO:0010040 response to iron(II) ion
GO:0010517 regulation of phospholipase activity
GO:0010642 negative regulation of platelet-derived growth factor receptor signaling pathway
GO:0014048 regulation of glutamate secretion
GO:0014059 regulation of dopamine secretion
GO:0016079 synaptic vesicle exocytosis
GO:0016082 synaptic vesicle priming
GO:0022898 regulation of transmembrane transporter activity
GO:0031115 negative regulation of microtubule polymerization
GO:0031623 receptor internalization
GO:0031648 protein destabilization
GO:0032026 response to magnesium ion
GO:0032410 negative regulation of transporter activity
GO:0032496 response to lipopolysaccharide
GO:0032769 negative regulation of monooxygenase activity
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0034341 response to type II interferon
GO:0034599 cellular response to oxidative stress
GO:0035493 SNARE complex assembly
GO:0035543 positive regulation of SNARE complex assembly
GO:0040012 regulation of locomotion
GO:0042416 dopamine biosynthetic process
GO:0042417 dopamine metabolic process
GO:0042775 mitochondrial ATP synthesis coupled electron transport
GO:0043030 regulation of macrophage activation
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043524 negative regulation of neuron apoptotic process
GO:0045807 positive regulation of endocytosis
GO:0045920 negative regulation of exocytosis
GO:0045921 positive regulation of exocytosis
GO:0046928 regulation of neurotransmitter secretion
GO:0048168 regulation of neuronal synaptic plasticity
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0048488 synaptic vesicle endocytosis
GO:0048489 synaptic vesicle transport
GO:0050729 positive regulation of inflammatory response
GO:0050806 positive regulation of synaptic transmission
GO:0050808 synapse organization
GO:0050812 regulation of acyl-CoA biosynthetic process
GO:0051259 protein complex oligomerization
GO:0051262 protein tetramerization
GO:0051281 positive regulation of release of sequestered calcium ion into cytosol
GO:0051402 neuron apoptotic process
GO:0051583 dopamine uptake involved in synaptic transmission
GO:0051585 negative regulation of dopamine uptake involved in synaptic transmission
GO:0051612 negative regulation of serotonin uptake
GO:0051621 regulation of norepinephrine uptake
GO:0051622 negative regulation of norepinephrine uptake
GO:0055074 calcium ion homeostasis
GO:0060079 excitatory postsynaptic potential
GO:0060291 long-term synaptic potentiation
GO:0060732 positive regulation of inositol phosphate biosynthetic process
GO:0061024 membrane organization
GO:0070495 negative regulation of thrombin-activated receptor signaling pathway
GO:0070555 response to interleukin-1
GO:0071280 cellular response to copper ion
GO:0071872 cellular response to epinephrine stimulus
GO:0071902 positive regulation of protein serine/threonine kinase activity
GO:0097435 supramolecular fiber organization
GO:1902957 negative regulation of mitochondrial electron transport, NADH to ubiquinone
GO:1903284 positive regulation of glutathione peroxidase activity
GO:1903285 positive regulation of hydrogen peroxide catabolic process
GO:1903421 regulation of synaptic vesicle recycling
GO:1903426 regulation of reactive oxygen species biosynthetic process
GO:1904377 positive regulation of protein localization to cell periphery
GO:1904715 negative regulation of chaperone-mediated autophagy
GO:1905606 regulation of presynapse assembly
GO:1990000 amyloid fibril formation
GO:2000377 regulation of reactive oxygen species metabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005764 lysosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005938 cell cortex
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0016234 inclusion body
GO:0030424 axon
GO:0030426 growth cone
GO:0030672 synaptic vesicle membrane
GO:0031092 platelet alpha granule membrane
GO:0032991 protein-containing complex
GO:0042995 cell projection
GO:0043025 neuronal cell body
GO:0043679 axon terminus
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0098794 postsynapse
GO:0099512 supramolecular fiber

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7ynm, PDBe:7ynm, PDBj:7ynm
PDBsum7ynm
PubMed
UniProtP37840|SYUA_HUMAN Alpha-synuclein (Gene Name=SNCA)

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