Structure of PDB 8tkh Chain D Binding Site BS03

Receptor Information

>8tkh Chain D (length=2268) Species: 9606 (Homo sapiens)

SSFLHIGDIVSLYAEGSVNGFISTLGLVDDRCVVEPAAGDLDNPPKKFRD
CLFKVCPMNRYSAQKQYWKAKQTDVVLLQKLQHAAQMEQKQNDTENKKVH
GDVVKYGSVIQLLHMKSNKYLTVNKRLPALLEKNAMRVTLDATGNEGSWL
FIQPFWKLRSNGDNVVVGDKVILNPVNAGQPLHASNYELSDNAGCKEVNS
VNCNTSWKINLFMQFRDHLEEVLKGGDVVRLFHAEQEKFLTCDEYKGKLQ
VFLRTTLRQSATSATSSNALWEVEVVHHDPCRGGAGHWNGLYRFKHLATG
NYLAAEENPSIKYCLVAVPHGNDIASLFELDPTTLQKTDSFVPRNSYVRL
RHLCTNTWIQSTNVPIDIEEERPIRLMLGTCPTKEDKEAFAIVSVPVSEI
RDLDFANDASSMLASAVEKLNEGFISQNDRRFVIQLLEDLVFFVSDVPNN
GQNVLDIMVTKPNRERQKLMREQNILKQVFGILKAPFRPLVRLEELSDQK
NAPYQHMFRLCYRVLRHSQEDYRKNQEHIAKQFGMMQSQIGYDILAEDTI
TALLHNNRKLLEKHITKTEVETFVSLVRKNREPRFLDYLSDLCVSNHIAI
PVTQELICKCVLDPKNSDILIRTELRPVEEEVWLTWTDKNNEHHEKSVRQ
LAQEARAGNAHDENVLSYYRYQLKLFARMCLDRQYLAIDEISQQLGVDLI
FLCMADEMLPFDLRASFCHLMLHVHVDRDPQELVTPVKFARLWTEIPTAI
TIKDYDSNLNASRDDKKNKFANTMEFVEDYLNNVVSEAVPFANEEKNKLT
FEVVSLAHNLIYFGFYSFSELLRLTRTLLGIIDCVTMVLSRKQSVFSAPS
LSAENEDIVVMETKLKILEILQFILNVRLDYRISYLLSVFKKEFVEVFPN
MNLDRIGEQAEAMFGVGKTSSMLEVDDEGGRMFLRVLIHLTMHDYAPLVS
GALQLLFKHFSQRQEAMHTFKQVQLLISAQDVENYKVIKSELDRLRTMVE
KSELWVSENYQIVKGILERLNKMCGVGEQMRKKQQRLLKNMDAHKVMLDL
LQIPYDKGDAKMMEILRYTHQFLQKFCAGNPGNQALLHKHLHLFLTPGLL
EAETMQHIFLNNYQLCSEISEPVLQHFVHLLATHGRHVQYLDFLHTVIKA
EGKYVKKCQDMIMTELTNAGDDVVVFYNDKASLAHLLDMMKAARDGVEDH
SPLMYHISLVDLLAACAEGKNVYTEIKCTSLLPLEDVVSVVTHEDCITEV
KMAYVNFVNHCYVDTEVEMKEIYTSNHIWTLFENFTLDMARVCSKREKRV
ADPTLEKYVLSVVLDTINAFFSSPFSENSTSLQTHQTIVVQLLQSTTRLL
ECPWLQQQHKGSVEACIRTLAMVAKGRAILLPMDLDAHISSMLSWDYKNI
IEKLQDIITALEERLKPLVQAELSVLVDVLHWPELLFLEGSEAYQRCESG
GFLSKLIQHTKDLMESEEKLCIKVLRTLQQMLLKKTKYGDRGNQLRKMLL
QNYLQNRDWSAIAATQCRLDKEGATKLVCDLITSTKNEKIFQESIGLAIH
LLDGGNTEIQKSFHNLMMSDKKSERFFKVLHDRMKRAQQETKSTVEMGTS
VLIMQPILRFLQLLCENHNRDLQNFLRCQNNKTNYNLVCETLQFLDIMCG
STTGGLGLLGLYINEDNVGLVIQTLETLTEYCQGPCHENQTCIVTHESNG
IDIITALILNDISPLCKYRMDLVLQLKDNASKLLLALMESRHDSENAERI
LISLRPQELVDVIKKAYLQEEERENSEVSPREVGHNIYILALQLSRHNKQ
LQHLLKPVEDPLAYYENHTSQIEIVRQDRSMEQIVFPVPGICQFLTEETK
HRLFTTTEQDEQGSKVSDFFDQSSFLHNEMEWQRKLRSMPLIYWFSRRMT
LWGSISFNLAVFINIIIAFFYPYMSIRPLIVALILRSIYYLGIGPTLNIL
GALNLTNKIVFVVSFVGNRGTFIRGYKAMVMDMEFLYHVGYILTSVLGLF
AHELFYSILLFDLIYREETLFNVIKSVTRNGRSILLTALLALILVYLFSI
VGFLFLKDDFILEVDRLPDSTERACDTLLMCIVTVMNHGLRNGGGVGDIL
RKPSKDESLFPARVVYDLLFFFIVIIIVLNLIFGVIIDTFADLRSEKQKK
EEILKTTCFICGLERDKFDNKTVSFEEHIKLEHNMWNYLYFIVLVRVKNK
TDYTGPESYVAQMIKNKNLDWFPRMRAMSLVSNEGEGEQNEIRILQDKLN
STMKLVSHLTAQLNELKE

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 8tkh Chain D Residue 3003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8tkh Structural titration reveals Ca 2+ -dependent conformational landscape of the IP 3 receptor.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): F2539 I2559 K2560 H2563 N2564 M2565 W2566
• Binding residue (residue number reindexed from 1): F2159 I2179 K2180 H2183 N2184 M2185 W2186
• Annotation score: 1

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

External links

• PDB: RCSB:8tkh, PDBe:8tkh, PDBj:8tkh
• PDBsum: 8tkh
• PubMed: 37898605
• UniProt: Q14573|ITPR3_HUMAN Inositol 1,4,5-trisphosphate-gated calcium channel ITPR3 (Gene Name=ITPR3)