Structure of PDB 8tkf Chain D Binding Site BS02

Receptor Information
>8tkf Chain D (length=2272) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPKKFRD
CLFKVCPMNRYSAQKQYWKAKQDVVLLQKLQHAAQMEQKQNDTENKKVHG
DVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRVTLDATGNEGSWLF
IQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYELSDNAGCKEVNSV
NCNTSWKINLFMQFRDHLEEVLKGGDVVRLFHAEQEKFLTCDEYKGKLQV
FLRTTLRQSATSATSSNALWEVEVVHHDPCRGGAGHWNGLYRFKHLATGN
YLAAEENPSYEKIKYCLVAVPHGNDIASLFELDPTTLQKTDSFVPRNSYV
RLRHLCTNTWIQSTNVPIDIEEERPIRLMLGTCPTKEDKEAFAIVSVPVS
EIRDLDFANDASSMLASAVEKLNEGFISQNDRRFVIQLLEDLVFFVSDVP
NNGQNVLDIMVTKPNRERQKLMREQNILKQVFGILKAPFRPLVRLEELSD
QKNAPYQHMFRLCYRVLRHSQEDYRKNQEHIAKQFGMMQSQIGYDILAED
TITALLHNNRKLLEKHITKTEVETFVSLVRKNREPRFLDYLSDLCVSNHI
AIPVTQELICKCVLDPKNSDILIRTELRPEEVWLTWTDKNNEHHEKSVRQ
LAQEARAGNAHDENVLSYYRYQLKLFARMCLDRQYLAIDEISQQLGVDLI
FLCMADEMLPFDLRASFCHLMLHVHVDRDPQELVTPVKFARLWTEIPTAI
TIKDYDSNLNASRDDKKNKFANTMEFVEDYLNNVVSEAVPFANEEKNKLT
FEVVSLAHNLIYFGFYSFSELLRLTRTLLGIIDDIVVMETKLKILEILQF
ILNVRLDYRISYLLSVFKKEFVEVFPNLDRIGEQAEAMFGSMLEVDDEGG
RMFLRVLIHLTMHDYAPLVSGALQLLFKHFSQRQEAMHTFKQVQLLISAQ
DVENYKVIKSELDRLRTMVEKSELWVDSENYQIVKGILERLNKMCGVGEQ
MRKKQQRLLKNMDAHKVMLDLLQIPYDKGDAKMMEILRYTHQFLQKFCAG
NPGNQALLHKHLHLFLTPGLLEAETMQHIFLNNYQLCSEISEPVLQHFVH
LLATHGRHVQYLDFLHTVIKAEGKYVKKCQDMIMTELTNAGDDVVVFYND
KASLAHLLDMMKAARDGVEDHSPLMYHISLVDLLAACAEGKNVYTEIKCT
SLLPLEDVVSVVTHEDCITEVKMAYVNFVNHCYVDTEVEMKEIYTSNHIW
TLFENFTLDMARVCSKREKRVADPTLEKYVLSVVLDTINAFFSSPFSENS
TSLQTHQTIVVQLLQSTTRLLECPWLQQQHKGSVEACIRTLAMVAKGRAI
LLPMDLDAHISSMLSSGASDYKNIIEKLQDIITALEERLKPLVQAELSVL
VDVLHWPELLFLEGSEAYQRCESGGFLSKLIQHTKDLMESEEKLCIKVLR
TLQQMLLKKTKYGDRGNQLRKMLLQNYLQWSAIAATQCRLDKEGATKLVC
DLITSTKNEKIFQESIGLAIHLLDGGNTEIQKSFHNLMMSDKKSERFFKV
LHDRMKRAQQETKSTVMGTSVLIMQPILRFLQLLCENHNRDLQNFLRCQN
NKTNYNLVCETLQFLDIMCGSTTGGLGLLGLYINEDNVGLVIQTLETLTE
YCQGPCHENQTCIVTHESNGIDIITALILNDISPLCKYRMDLVLQLKDNA
SKLLLALMESRHDSENAERILISLRPQELVDVIKKAYLQEEERENSEVSP
REVGHNIYILALQLSRHNKQLQHLLKPVEDPLAYYENHTSQIEIVRQDRS
MEQIVFPVPGICQFLTEETKHRLFTTTEQDEQGSKVSDFFDQSSFLHNEM
EWQRKLRSMPLIYWFSRRMTLWGSISFNLAVFINIIIAFFYPYMSTGVLD
SPLISLLFWILICFSIAALFTKRYSIRPLIVALILRSIYYLGIGPTLNIL
GALNLTNKIVFVVSFVGNRGTFIRGYKAMVMDMEFLYHVGYILTSVLGLF
AHELFYSILLFDLIYREETLFNVIKSVTRNGRSILLTALLALILVYLFSI
VGFLFLKDDFILEVDRLPLDSTERACDTLLMCIVTVMNHGLRNGGGVGDI
LRKPSKDESLFPARVVYDLLFFFIVIIIVLNLIFGVIIDTFADLRSEKQK
KEEILKTTCFICGLERDKFDNKTVSFEEHIKLEHNMWNYLYFIVLVRVKN
KTDYTGPESYVAQMIKNKNLDWFPRMRAMSLVSNEGEGEQNEIRILQDKL
NSTMKLVSHLTAQLNELKEQMT
Ligand information
Ligand IDPT5
InChIInChI=1S/C47H85O19P3/c1-3-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-36-41(49)63-39(37-61-40(48)35-33-31-29-27-25-23-21-18-16-14-12-10-8-6-4-2)38-62-69(59,60)66-45-42(50)43(51)46(64-67(53,54)55)47(44(45)52)65-68(56,57)58/h11,13,17,19,22,24,28,30,39,42-47,50-52H,3-10,12,14-16,18,20-21,23,25-27,29,31-38H2,1-2H3,(H,59,60)(H2,53,54,55)(H2,56,57,58)/b13-11?,19-17?,24-22-,30-28?/t39-,42-,43+,44+,45-,46-,47-/m1/s1
InChIKeyCNWINRVXAYPOMW-HJBQCNPJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[CH]1[CH](O)[CH](O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OC1C(C(C(C(C1O)OP(=O)(O)O)OP(=O)(O)O)O)O)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[C@@H]1[C@H](O)[C@H](O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O)OC(=O)CCC\C=C/C\C=C/C/C=C/CC=CCCCCC
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)OP(=O)(O)O)OP(=O)(O)O)O)O)OC(=O)CCCC=CC/C=C\CC=CCC=CCCCCC
FormulaC47 H85 O19 P3
Name[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate;
Phosphatidylinositol 4,5-bisphosphate;
PtdIns(4,5)P2
ChEMBL
DrugBank
ZINC
PDB chain8tkf Chain D Residue 2701 [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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PDB8tkf Structural titration reveals Ca 2+ -dependent conformational landscape of the IP 3 receptor.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S2206 F2209 F2221 R2262 V2266 R2351 E2352
Binding residue
(residue number reindexed from 1)		S1874 F1877 F1889 R1927 V1931 R2016 E2017
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000822 inositol hexakisphosphate binding
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:0015278 intracellularly gated calcium channel activity
GO:0035091 phosphatidylinositol binding
GO:0043533 inositol 1,3,4,5 tetrakisphosphate binding
GO:0070679 inositol 1,4,5 trisphosphate binding
Biological Process
GO:0006811 monoatomic ion transport
GO:0006816 calcium ion transport
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007613 memory
GO:0019722 calcium-mediated signaling
GO:0030168 platelet activation
GO:0050909 sensory perception of taste
GO:0050913 sensory perception of bitter taste
GO:0050916 sensory perception of sweet taste
GO:0050917 sensory perception of umami taste
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051289 protein homotetramerization
GO:0051592 response to calcium ion
GO:0055074 calcium ion homeostasis
GO:0055085 transmembrane transport
GO:0060291 long-term synaptic potentiation
GO:0070588 calcium ion transmembrane transport
Cellular Component
GO:0005634 nucleus
GO:0005640 nuclear outer membrane
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0005903 brush border
GO:0016020 membrane
GO:0016529 sarcoplasmic reticulum
GO:0030658 transport vesicle membrane
GO:0030667 secretory granule membrane
GO:0031095 platelet dense tubular network membrane
GO:0031410 cytoplasmic vesicle
GO:0043025 neuronal cell body
GO:0043235 receptor complex
GO:0045177 apical part of cell
GO:0098554 cytoplasmic side of endoplasmic reticulum membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8tkf, PDBe:8tkf, PDBj:8tkf
PDBsum8tkf
PubMed37898605
UniProtQ14573|ITPR3_HUMAN Inositol 1,4,5-trisphosphate-gated calcium channel ITPR3 (Gene Name=ITPR3)

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