Structure of PDB 8sep Chain A Binding Site BS01

Receptor Information

>8sep Chain A (length=4379) Species: 9986 (Oryctolagus cuniculus)

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
AELLGMDLASLEIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFF
FAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNF
FRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDE
YELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKC
FICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQES
YVWKMYQERCWDFFPAGDCFRKQYEDQLS

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8sep Chain A Residue 5101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8sep Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.
• Resolution: 3.57 Å
• Binding residue (original residue number in PDB): M4954 C4958 F4959 T4979 H4983 L4985
• Binding residue (residue number reindexed from 1): M4296 C4300 F4301 T4321 H4325 L4327
• Annotation score: 1

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

External links

• PDB: RCSB:8sep, PDBe:8sep, PDBj:8sep
• PDBsum: 8sep
• PubMed: 37192614
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)