Structure of PDB 7k0s Chain B Binding Site BS01

Receptor Information
>7k0s Chain B (length=4110) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPD
LAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTT
SRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVS
VSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLF
HGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSH
LRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL
DTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLK
KKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSG
KPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRN
RQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLY
ELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPE
VLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITE
NLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVP
FLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWT
GHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNL
DGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRL
EPIKEYRREGPRGPHLVGPSRCLSHTDFHLERIREKLAENIHELWALTRI
EQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETLKTLLALGC
HVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVRLTPAQTTLVDR
LAENGHNVWARDRVAQGWSYSARLLDEATKRSNRDSLCQAVRTLLGYGYN
IEDRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGA
DELAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGE
VLMSDSGSETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAIC
GLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTP
PCLRLAHRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSR
MPNHFLQERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHS
HTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDL
LISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRHGLPG
VGVTTSLRPPHHFSPPCFVAVAEAPARLSPAIPLEALRDKALRMLGEAVR
DGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEV
FTEELEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVD
KLQANQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDEAD
EEDCPLPEDIRQDLQDFHQDLLAHCGIQLEGKKPQSLQELVSHMVVRWAQ
EDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLE
CLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETV
MEVMVNVLGGGETKEIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYL
LENSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGL
QSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLL
IRKPECFGPALRGEGGSGLLAAIEEAIRISEDPARNRVHLGHAIMSFYAA
LIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPT
LAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAANFDPRPVETLNVIIPEKLDSFINKFAEYTHEK
WAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKA
MIAWESRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLT
AKEKARDREKAQELLKFLQMNGYAVTRAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATPLYNLPTHRA
CNMFLESYKAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLH
QLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGENEEVEVSFE
EKEMEKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISI
LNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAE
GLGMVNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLR
TQTGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKA
MSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLA
QDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSN
VEMILKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFT
GPEIQFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHV
PHDPRLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQ
WEMPQVKESKRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEF
WGELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPGNM
VYYFLEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKEL
ARKLEFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDK
HGDIFGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQI
WKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTIL
SSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCD
DMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVI
LLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFET
HTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDC
FRKQYEDQLS
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain7k0s Chain B 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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PDB7k0s Molecular Mechanism of Inhibition of RyR1 by Magnesium
Resolution4.5 Å
Binding residue
(original residue number in PDB)		K4211 T4979 H4983 N4984 L4985
Binding residue
(residue number reindexed from 1)		K3607 T4052 H4056 N4057 L4058
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Feb 21 20:27:56 2025

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()
   1435     title=pdb2title(pdbid)
   1436     if bs.startswith("BS"):
=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1438     else:
   1439         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '7k0s', asym_id = 'B', bs = 'BS01', title = 'Molecular Mechanism of Inhibition of RyR1 by Magnesium'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7k0s', asym_id='B', bs='BS01', title='Molecular Mechanism of Inhibition of RyR1 by Magnesium')
   1295         display_ec(ec,csaOrig,csaRenu)
   1296     if go:
=> 1297         display_go(go,uniprot,pdbid,asym_id)
   1298     return pubmed,uniprot
   1299 
global display_go = <function display_go>, go = '0005216,0005219,0005262,0006811,0006816,0006874,0016020,0055085,0070588', uniprot = '', pdbid = '7k0s', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005216,0005219,0005262,0006811,0006816,0006874,0016020,0055085,0070588', uniprot='', pdbid='7k0s', asym_id='B')
    480         '''.replace("$namespace_link",namespace_link
    481           ).replace("$namespace",namespace
=>  482           ).replace("$uniprot",u
    483         ))
    484         for l,(term,name) in enumerate(go2aspect[Aspect]):
u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>