Structure of PDB 8ear Chain B Binding Site BS04

Receptor Information
>8ear Chain B (length=2389) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSFLHIGDICSLYAEGSTNGFISTLGLVDDRCVVQPEAGDLNNPPKKFRD
CLFKLCPMNRYSAQKQFWKAAKPGANSTTDAVLLNKLHHAADLEKKQNET
ENRKLLGTVIQYGNVIQLLHLKSNKYLTVNKRLPALLEKNAMRVTLDEAG
NEGSWFYIQPFYKLRSIGDSVVIGDKVVLNPVNAGQPLHASSHQLVDNPG
CNEVNSVNCNTSWKIVLFMKWSDNKDDILKGGDVVRLFHAEQEKFLTCDE
HRKKQHVFLRTTGRQSATSATSSKALWEVEVVQHDPCRGGAGYWNSLFRF
KHLATGHYLAAEVDPDFKMVYSLVSVPEGNDISSIFELDPTTLRGGDSLV
PRNSYVRLRHLCTNTWVHSTNIPIDKEEEKPVMLKIGTSPLKEDKEAFAI
VPVSPAEVRDLDFANDASKVLGSIAGKLEKGTITQNERRSVTKLLEDLVY
FVTGGTNSGQDVLEVVFSKPNRERQKLMREQNILKQIFKLLQAPFTDCGD
GPMLRLEELGDQRHAPFRHICRLCYRVLRHSQQDYRKNQEYIAKQFGFMQ
KQIGYDVLAEDTITALLHNNRKLLEKHITAAEIDTFVSLVRKNREPRFLD
YLSDLCVSMNKSIPVTQELICKAVLNPTNADILIETKLVLSRFEEEVWLF
WRDSNKEIRSKSVRELAQDAKEGQKEDRDVLSYYRYQLNLFARMCLDRQY
LAINEISGQLDVDLILRCMSDENLPYDLRASFCRLMLHMHVDRDPQEQVT
PVKYARLWSEIPSEIAIDDYDSSGASKDEIKERFAQTMEFVEEYLRDVVC
QRFPFSDKEKNKLTFEVVNLARNLIYFGFYNFSDLLRLTKILLAILDCVH
VPEKEDIMVMDTKLKIIEILQFILNVRLDYRISCLLCIFKREFDESNSQS
PGALDFEHIEEQAEGIFGGSEENTPLDLDDHGGRTFLRVLLHLTMHDYPP
LVSGALQLLFRHFSQRQEVLQAFKQVQLLVTSQDVDNYKQIKQDLDQLRS
IVEKSELWVYKGESTSSYNYRVVKEILIRLSKLCVQESASVRKSRKQQQR
LLRNMGAHAVVLELLQIPYEKAEDTKMQEIMRLAHEFLQNFCAGNQQNQA
LLHKHINLFLNPGILEAVTMQHIFMNNFQLCSEINERVVQHFVHCIETHG
RNVQYIKFLQTIVKAEGKFIKKCQDMVMAELVNSGEDVLVFYNDRASFQT
LIQMMRSERDRMDENSPLFMYHIHLVELLAVCTEGKNVYTEIKCNSLLPL
DDIVRVVTHEDCIPEVKIAYINFLNHCYVDTEVEMKEIYTSNHMWKLFEN
FLVDICRACNNTSDRKHADSVLEKYVTEIVMSIVTTFFSSPFSDQSTTLQ
TRQPVFVQLLQGVFRVYHCNWLMPSQKASVESCIRVLSDVAKSRAIAIPV
DLDSQVNNLFLKSSVLAASRDYRNIIERLQDIVSALEDRLRPLVQAELSV
LVDVLHRPELLFPENTDARRKCESGGFICKLIKHTKQLLEENEEKLCIKV
LQTLREMMTKDRGPPLRQLEDHKRGEALRQILVNRYYGNISTSRGEMSLA
EVQCHLDKEGASNLVIDLIMNASSDRVFHESILLAIALLEGGNTTIQHSF
FCRLTEDKKSEKFFKVFYDRMKVAQQEIKATVTVNTSDLGNKKDDLEMSA
VITIMQPILRFLQLLCENHNRDLQNFLRCQNNKTNYNLVCETLQFLDCIC
GSTTGGLGLLGLYINEKNVALINQTLESLTEYCQGPCHENQNCIATHESN
GIDIITALILNDINPLGKKRMDLVLELKNNASKLLLAIMESRHDSENAER
ILYNMRPKELVEVIKKAYMQGEVEFEDGENGEDGAASPRNVGHNIYILAH
QLARHNKELQTMLKPGGQVDGDEALEFYAKHTAQIEIVRLDRTMEQIVFP
VPSICEFLTKESKLRIYYTTERDEQGSKINDFFLRSEDLFNEMNWQKKLR
AQPVLYWCARNMSFWSSISFNLAVLMNLLVAFFYPFKGVRGGTLEPHWSG
LLWTAMLISLAIVIALPKPHGIRALIASTILRLIFSVGLQPTLFLLGAFN
VCNKIIFLMSFVGNCGTFTRGYRAMVLDVEFLYHLLYLLICAMGLFVHEF
FYSLLLFDLVYREETLLNVIKSVTRNGRPIILTAALALILVYLFSIVGYL
FFKDDFILEVDRLPNETAEQDKEHTCETLLMCIVTVLSHGLRSGGGVGDV
LRKPSKEEPLFAARVIYDLLFFFMVIIIVLNLIFGVIIDTFADLRSEKQK
KEEILKTTCFICGLERDKFDNKTVTFEEHIKEEHNMWHYLCFIVLVKVKD
STEYTGPESYVAEMIRERNLDWFPRMRAMSLVSSDSEGEQNELRNLQEKL
ESTMKLVTNLSGQLSELKDQMTEQRKQKQRIGLLGHPPH
Ligand information
Ligand IDI3P
InChIInChI=1S/C6H15O15P3/c7-1-2(8)5(20-23(13,14)15)6(21-24(16,17)18)3(9)4(1)19-22(10,11)12/h1-9H,(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)/t1-,2+,3+,4-,5-,6-/m1/s1
InChIKeyMMWCIQZXVOZEGG-XJTPDSDZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OC1C(O)C(O)C(OP(=O)(O)O)C(O)C1OP(=O)(O)O)(O)O
OpenEye OEToolkits 1.5.0C1(C(C(C(C(C1OP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O)[CH]1O[P](O)(O)=O
OpenEye OEToolkits 1.5.0[C@H]1([C@@H]([C@H]([C@@H]([C@H]([C@@H]1OP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@@H]1[C@H](O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@@H]1O[P](O)(O)=O
FormulaC6 H15 O15 P3
NameD-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
ChEMBLCHEMBL279107
DrugBankDB03401
ZINCZINC000004095598
PDB chain8ear Chain B Residue 2804 [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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PDB8ear Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		R265 Y567 K569
Binding residue
(residue number reindexed from 1)		R260 Y535 K537
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005216 monoatomic ion channel activity
GO:0005220 inositol 1,4,5-trisphosphate-gated calcium channel activity
GO:0005262 calcium channel activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0015278 intracellularly gated calcium channel activity
GO:0019855 calcium channel inhibitor activity
GO:0019903 protein phosphatase binding
GO:0019904 protein domain specific binding
GO:0035091 phosphatidylinositol binding
GO:0042802 identical protein binding
GO:0044325 transmembrane transporter binding
GO:0044877 protein-containing complex binding
GO:0046872 metal ion binding
GO:0070679 inositol 1,4,5 trisphosphate binding
GO:0098695 inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels
Biological Process
GO:0000902 cell morphogenesis
GO:0001666 response to hypoxia
GO:0006811 monoatomic ion transport
GO:0006816 calcium ion transport
GO:0006915 apoptotic process
GO:0007200 phospholipase C-activating G protein-coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007207 phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway
GO:0007338 single fertilization
GO:0009791 post-embryonic development
GO:0010976 positive regulation of neuron projection development
GO:0016358 dendrite development
GO:0019722 calcium-mediated signaling
GO:0032024 positive regulation of insulin secretion
GO:0032469 endoplasmic reticulum calcium ion homeostasis
GO:0036444 calcium import into the mitochondrion
GO:0042045 epithelial fluid transport
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0050849 negative regulation of calcium-mediated signaling
GO:0050882 voluntary musculoskeletal movement
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051289 protein homotetramerization
GO:0051480 regulation of cytosolic calcium ion concentration
GO:0051928 positive regulation of calcium ion transport
GO:0055085 transmembrane transport
GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
GO:0070588 calcium ion transmembrane transport
GO:0071320 cellular response to cAMP
GO:0071456 cellular response to hypoxia
GO:0097421 liver regeneration
GO:0099105 ion channel modulating, G protein-coupled receptor signaling pathway
GO:0099566 regulation of postsynaptic cytosolic calcium ion concentration
GO:1903514 release of sequestered calcium ion into cytosol by endoplasmic reticulum
GO:1990806 ligand-gated ion channel signaling pathway
GO:2000347 positive regulation of hepatocyte proliferation
Cellular Component
GO:0005635 nuclear envelope
GO:0005637 nuclear inner membrane
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0005955 calcineurin complex
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016529 sarcoplasmic reticulum
GO:0030425 dendrite
GO:0030658 transport vesicle membrane
GO:0030667 secretory granule membrane
GO:0030868 smooth endoplasmic reticulum membrane
GO:0031088 platelet dense granule membrane
GO:0031094 platelet dense tubular network
GO:0031410 cytoplasmic vesicle
GO:0032991 protein-containing complex
GO:0043025 neuronal cell body
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0097060 synaptic membrane
GO:0098685 Schaffer collateral - CA1 synapse
GO:0098793 presynapse
GO:0098794 postsynapse
GO:0098982 GABA-ergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ear, PDBe:8ear, PDBj:8ear
PDBsum8ear
PubMed36376291
UniProtP29994|ITPR1_RAT Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1 (Gene Name=Itpr1)

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