Structure of PDB 8seo Chain C Binding Site BS01

Receptor Information
>8seo Chain C (length=4376) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPP
DLAICCFTLEQSLSVRALQEMLANHRTLLYGHAILLRHAHSRMYLSCLTT
SRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLF
HGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSH
LRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL
PKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKKA
ILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSGKPR
GSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQS
LFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLYELL
ASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPEVLN
IIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLL
PGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFLT
AQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGHV
ARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDGL
FFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRLEPI
KEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREKLAE
NIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSG
ETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVR
LTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRL
LDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVENQSRWDRVRIFR
AEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFNG
HRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSE
TAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPF
AINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRT
WGSQNSLVEMLFLRLSLPVQFHQHFRCTDNRDDPEIILNTTTYYYSVRVF
AGQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCS
NCYMVWGGDFVSPGQQGRISHTDLVIGCLVDLATGLMTFTANGKESNTFF
QVEPNTKLFPAVFVLPTHQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQ
CPPRLEVQMLMPVSWSRMPNHFLQVETRRAGERLGWAVQCQDPLTMMALH
IPEENRCMDILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVD
QAQLLHALEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTP
ETRAITLFPPGRKGGNARRHGLPGVGVTTSLRPPHHFSPPCFVAALPAAG
VAEAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVP
VLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEELEEGLLQMKLPESVKL
QMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTMS
AAETARRTREFRSPPQEQINMLLHFKDEADEEDCPLPEDIRQDLQDFHQD
LLAHCGIQLEKKPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQY
DGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEENLM
IQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGGGETKEIRFPKM
VTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAA
SVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGG
ERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLA
AIEEAIRISEDPARDGPGVPPEENRVHLGHAIMSFYAALIDLLGRCAPEM
HLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGALVQPKM
SASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASLDTAT
FSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTVYRLS
RGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEFAKMP
LKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSLAHKK
YDQELYRMAMPCLCAIAGALPPDYVDASYSSKAEKNFDPRPVETLNVIIP
EKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFS
EKDKEIYRWPIKESLKAMIAWEWTIEKAREGEYNPQPPDLSGVTLSRELQ
AMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDREK
AQELLKFLQMNGYAVTRLDTSSIEKRFAFGFLQQLLRWMDISQEFIAHLE
AVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGSG
GHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDAR
TVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKVSKGVGQNLTYTTV
ALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTKNTYVE
KLRPALGECLARLAAAMPVAFLEPQLNEYNACSVYTTKSPRERAILGLPN
SVEEMCPDIPVLDRLMADIGGLAESGARYTEMPHVIEITLPMLCSYLPRW
WERGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEATW
MKRLAVFAQPIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRLEAK
AEAEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEEL
FRMVGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTADSKSKMARRGDR
YSVQTSLIVATLKKMLPIGLNMCAPTDQDLIMLAKTRYALKDTDEEVREF
LQNNLHLQGKVEGSPSLRWQMALYRGLPGREEDADDPEKIVRRVQEVSAV
LYHLEQTEHPYKSKKAVWHKLLSKQRRRAVVACFRMTPLYNLPTHRACNM
FLESYKAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLHQLV
LHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEVEVSFEEKEMEKQRLL
YQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQ
KMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGT
VINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTIN
IIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNS
LTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLK
ELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDM
FLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSC
SEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFL
ELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESK
RQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEPFWGELEVQRV
KFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPNMVYYFLEESTG
YMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLY
ITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERI
AELLGMDLASDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAA
HLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRK
FYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYEL
YRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFIC
GIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVW
KMYQERCWDFFPAGDCFRKQYEDQLS
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain8seo Chain C Residue 5101 [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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PDB8seo Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.
Resolution3.92 Å
Binding residue
(original residue number in PDB)		M4954 C4958 F4959 T4979 L4985
Binding residue
(residue number reindexed from 1)		M4293 C4297 F4298 T4318 L4324
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005216 monoatomic ion channel activity
GO:0005219 ryanodine-sensitive calcium-release channel activity
GO:0005245 voltage-gated calcium channel activity
GO:0005262 calcium channel activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005524 ATP binding
GO:0015278 intracellularly gated calcium channel activity
GO:0015643 toxic substance binding
GO:0035381 ATP-gated ion channel activity
GO:0042802 identical protein binding
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
GO:0097718 disordered domain specific binding
Biological Process
GO:0003151 outflow tract morphogenesis
GO:0006811 monoatomic ion transport
GO:0006816 calcium ion transport
GO:0006874 intracellular calcium ion homeostasis
GO:0006936 muscle contraction
GO:0006941 striated muscle contraction
GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0019722 calcium-mediated signaling
GO:0043588 skin development
GO:0043931 ossification involved in bone maturation
GO:0048741 skeletal muscle fiber development
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051289 protein homotetramerization
GO:0055085 transmembrane transport
GO:0070588 calcium ion transmembrane transport
GO:0071277 cellular response to calcium ion
GO:0071313 cellular response to caffeine
Cellular Component
GO:0005790 smooth endoplasmic reticulum
GO:0014802 terminal cisterna
GO:0016020 membrane
GO:0016529 sarcoplasmic reticulum
GO:0030018 Z disc
GO:0031090 organelle membrane
GO:0033017 sarcoplasmic reticulum membrane
GO:0034704 calcium channel complex
GO:0042383 sarcolemma
GO:1990425 ryanodine receptor complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8seo, PDBe:8seo, PDBj:8seo
PDBsum8seo
PubMed37192614
UniProtP11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)

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