Structure of PDB 6nt3 Chain A Binding Site BS04

Receptor Information
>6nt3 Chain A (length=1278) Species: 6978,9606 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANKDRDGSAHPDQALEQGSRLPARMRNIFPAELASNKKTFVVVTKASGEK
SLWMLDPFTPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYIL
ELVFLSIYTIEVVVKVLARGFILHPFAYLRDPWNWLDFLVTLIGYITLVV
DLGHLYALRAFRVLRSWRTVTIVPGWRTIVDALSLSITSLKDLVLLLLFS
LSVFALIGLQLFMGNLKHKCVKHFPADGSWGNFTDERWFNYTSNSSHWYI
PDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFLSV
FRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMS
YTHMVKRADEEKAAECVPWQKLQGAIGAVVLSPFFELFIAVIIVLNITFM
ALDHHDMNIEFERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVF
DFIIVVFAILELGLEGVQGLSVFRSFRLLRVFRLAKFWPTLNNFMSVMTK
SYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMERFPDGDLPRWNFTD
FLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFFVGNLVILNLL
IALLLNNYGSVQRMWSNIRRVCFLLAKNKYFQKFVTAVLVITSVLLALED
IYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKYFTSKWYWLDF
IVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQVVTSTLVE
AVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITMDR
NDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVH
KQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSA
TDSRTQLIYRRAVMRTMSAKPVKRIPKPGNKIQGCIFDLVTNQAFDISIM
VLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHY
YFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILR
LVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHIRDA
GAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGY
PGNCGSRALGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEGLTD
DDYDMFFEVWQQFDPEATQYIRYDQLSELLEALQPPLQVQKPNKYKILSM
NIPICKDDHIFYKDVLEALVKDVFSRRG
Ligand information
Ligand IDAJP
InChIInChI=1S/C56H92O29/c1-19-7-10-56(75-17-19)20(2)31-45(85-56)37(67)32-22-6-5-21-11-26(24(61)12-55(21,4)23(22)8-9-54(31,32)3)76-50-42(72)39(69)44(30(16-60)80-50)81-53-48(47(36(66)29(15-59)79-53)83-49-40(70)33(63)25(62)18-74-49)84-52-43(73)46(35(65)28(14-58)78-52)82-51-41(71)38(68)34(64)27(13-57)77-51/h19-53,57-73H,5-18H2,1-4H3/t19-,20+,21+,22-,23+,24-,25-,26-,27-,28-,29-,30-,31+,32-,33+,34-,35+,36-,37+,38+,39-,40-,41-,42-,43-,44+,45-,46+,47+,48-,49+,50-,51+,52+,53+,54-,55+,56-/m1/s1
InChIKeyUVYVLBIGDKGWPX-KUAJCENISA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC1C2C(OC31CCC(C)CO3)C(O)C1C3CCC4CC(OC5OC(CO)C(OC6OC(CO)C(O)C(OC7OCC(O)C(O)C7O)C6OC6OC(CO)C(O)C(OC7OC(CO)C(O)C(O)C7O)C6O)C(O)C5O)C(O)CC4(C)C3CCC21C
CACTVS 3.385C[CH]1CC[C]2(OC1)O[CH]3[CH](O)[CH]4[CH]5CC[CH]6C[CH](O[CH]7O[CH](CO)[CH](O[CH]8O[CH](CO)[CH](O)[CH](O[CH]9OC[CH](O)[CH](O)[CH]9O)[CH]8O[CH]%10O[CH](CO)[CH](O)[CH](O[CH]%11O[CH](CO)[CH](O)[CH](O)[CH]%11O)[CH]%10O)[CH](O)[CH]7O)[CH](O)C[C]6(C)[CH]5CC[C]4(C)[CH]3[CH]2C
CACTVS 3.385C[C@@H]1CC[C@@]2(OC1)O[C@H]3[C@@H](O)[C@H]4[C@@H]5CC[C@H]6C[C@@H](O[C@@H]7O[C@H](CO)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O[C@@H]9OC[C@@H](O)[C@H](O)[C@H]9O)[C@H]8O[C@@H]%10O[C@H](CO)[C@H](O)[C@H](O[C@@H]%11O[C@H](CO)[C@@H](O)[C@H](O)[C@H]%11O)[C@H]%10O)[C@H](O)[C@H]7O)[C@H](O)C[C@]6(C)[C@H]5CC[C@]4(C)[C@H]3[C@@H]2C
OpenEye OEToolkits 2.0.7CC1CCC2(C(C3C(O2)C(C4C3(CCC5C4CCC6C5(CC(C(C6)OC7C(C(C(C(O7)CO)OC8C(C(C(C(O8)CO)O)OC9C(C(C(CO9)O)O)O)OC2C(C(C(C(O2)CO)O)OC2C(C(C(C(O2)CO)O)O)O)O)O)O)O)C)C)O)C)OC1
OpenEye OEToolkits 2.0.7C[C@@H]1CC[C@@]2([C@H]([C@H]3[C@@H](O2)[C@H]([C@@H]4[C@@]3(CC[C@H]5[C@H]4CC[C@@H]6[C@@]5(C[C@H]([C@@H](C6)O[C@H]7[C@@H]([C@H]([C@H]([C@H](O7)CO)O[C@H]8[C@@H]([C@H]([C@@H]([C@H](O8)CO)O)O[C@H]9[C@@H]([C@H]([C@@H](CO9)O)O)O)O[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O)O)O)C)C)O)C)OC1
FormulaC56 H92 O29
NameDigitonin
ChEMBL
DrugBank
ZINC
PDB chain6nt3 Chain A Residue 1620 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6nt3 Cryo-EM structures of a human-cockroach hybrid Nav channel in the presence and absence of the alpha-scorpion toxin AaH2.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		M999 R1074 N1085 Y1091 F1094
Binding residue
(residue number reindexed from 1)		M772 R847 N858 Y864 F867
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005216 monoatomic ion channel activity
GO:0005248 voltage-gated sodium channel activity
GO:0005261 monoatomic cation channel activity
Biological Process
GO:0006811 monoatomic ion transport
GO:0006814 sodium ion transport
GO:0055085 transmembrane transport
Cellular Component
GO:0001518 voltage-gated sodium channel complex
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6nt3, PDBe:6nt3, PDBj:6nt3
PDBsum6nt3
PubMed
UniProtD0E0C2|SCNA1_PERAM Sodium channel protein PaFPC1;
Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

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