Structure of PDB 7m6l Chain B Binding Site BS04

Receptor Information

>7m6l Chain B (length=4299) Species: 9986 (Oryctolagus cuniculus)

VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPP
DLAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLT
TSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILV
SVSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRL
FHGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGS
HLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEK
LPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKK
AILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSGKP
RGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQ
SLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLYEL
LASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPEVL
NIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENL
LPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFL
TAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGH
VARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDG
LFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRLEP
IKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREKLA
ENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMS
GETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHV
RLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYR
LLDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVENQSRWDRVRIF
RAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFN
GHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGS
ETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEP
FAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHR
TWGSQNSLVEMLFLRLSLPVQFHQHFRCTNRDDPEIILNTTTYYYSVRVF
AGQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCS
NCYMVWGGDFVRISHTDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNT
KLFPAVFVLPTHQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLE
VQMLMPVSWSRMPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENR
CMDILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLH
ALEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAIT
LFPPGRRHGLPGVGVTTSLRPPHHFSPPCFVAALAPARLSPAIPLEALRD
KALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDV
KQILKMIEPEVFTEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAA
FAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLL
HFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIPQSLQELVSHMVVRWA
QEDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLL
ECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHET
VMEVMVNVLGIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSQ
GSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGY
PDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPAL
RGEGGSGLLAAIEEAIRISEDPARDGPNRVHLGHAIMSFYAALIDLLGRC
APEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGALV
QPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASL
DTATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTV
YRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEF
AKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSL
AHKKYDQELYRMAMPCLCAIAGALPPDYVDASYSSKAEKNFDPRPVETLN
VIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPY
KTFSEKDKEIYRWPIKESLKAMIAWEWTIEKAREGEYNPQPPDLSGVTLS
RELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKAR
DREKAQELLKFLQMNGYAVTRSSIEKRFAFGFLQQLLRWMDISQEFIAHL
EAVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGS
GGHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDA
RTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKGVGQNLTYTTVAL
LPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTKNTYVEKL
RPALGECLARLAAAMPVAFLEPQLNEYNACSVYTTKSPRERAILGLPNSV
EEMCPDIPVLDRLMADIGGLAESGARYTEMPHVIEITLPMLCSYLPRWWE
RGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEATWMK
RLAVFAQPIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRLEAKAE
AEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEELFR
MVGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTYSVQTSLIVATLKKM
LPIGLNMCAPTDQDLIMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSP
SLRWQMALYRGLPGREEDADDPEKIVRRVQEVSAVLYHLEQTEHPYKSVV
ACFRMTPLYNLPTHRACNMFLESYKAAWILTEDHSFEDRMIDDLSKAGEK
KPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLVSFEEKEM
EKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGG
NAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGM
VNEDGTVIEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTI
NIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFN
SLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELL
KELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFD
MFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLS
CSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNF
LELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKES
KRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEFWGELEVQRV
KFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPMVYYFLEESTGY
MEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYI
TEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIA
ELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGVIFTDNS
FLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLV
MTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMY
VGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIID
AFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANY
MFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

Ligand information

• Ligand ID: CFF
• InChI: InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
• InChIKey: RYYVLZVUVIJVGH-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cn1cnc2N(C)C(=O)N(C)C(=O)c12
  ACDLabs 10.04: O=C2N(c1ncn(c1C(=O)N2C)C)C
  OpenEye OEToolkits 1.5.0: Cn1cnc2c1C(=O)N(C(=O)N2C)C
• Formula: C8 H10 N4 O2
• Name: CAFFEINE;
  3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE
• ChEMBL: CHEMBL113
• DrugBank: DB00201
• ZINC: ZINC000000001084
• PDB chain: 7m6l Chain B Residue 5304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m6l High-resolution structure of the membrane-embedded skeletal muscle ryanodine receptor.
• Resolution: 3.98 Å
• Binding residue (original residue number in PDB): F3753 E4239 W4716 I4996
• Binding residue (residue number reindexed from 1): F3345 E3826 W3978 I4258
• 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:7m6l, PDBe:7m6l, PDBj:7m6l
• PDBsum: 7m6l
• PubMed: 34469755
• UniProt: P11716|RYR1_RABIT Ryanodine receptor 1 (Gene Name=RYR1)