Structure of PDB 8f0p Chain A Binding Site BS01

Receptor Information
>8f0p Chain A (length=1116) Species: 6978,9606 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTI
EVVVKVLARGFILHPFAYLRDPWNWLDFLVTLIGYITLVVLYALRAFRVL
RSWRTVTIVPGWRTIVDALSLSITSLKDLVLLLLFSLSVFALIGLQLFMG
NLKHKCVKHFPADGSWGNFTDERWFNYTSNSSHWYIPDDWIEYPLCGNSS
GAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFLSVFRLVTLDYWEDLYQ
LALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRADEEKVV
LSPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYIFTSIYIVEA
VLKIIALSPKFYFKDSWNVFDFIIVVFAILELGLVFRSFRLLRVFRLAKF
WPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMER
FPDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVA
VFFVGNLVILNLLIALLLNNYGWSNIRRVCFLLAKNKYFQKFVTAVLVIT
SVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKYFT
SKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQ
VVTSTLVEAVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVL
SHEITMDRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMND
AIDSREVHKQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQR
RKAEGLSATDSRTQLIYRRAVMRTMSAKPVKRIPKNKIQGCIFDLVTNQA
FDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKL
ISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLAR
IGRILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFF
MHIRDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAP
DHELGYPGNCGSRALGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDS
KEGLTDDDYDMFFEVW
Ligand information
Ligand IDY01
InChIInChI=1S/C31H50O4/c1-20(2)7-6-8-21(3)25-11-12-26-24-10-9-22-19-23(35-29(34)14-13-28(32)33)15-17-30(22,4)27(24)16-18-31(25,26)5/h9,20-21,23-27H,6-8,10-19H2,1-5H3,(H,32,33)/t21-,23+,24+,25-,26+,27+,30+,31-/m1/s1
InChIKeyWLNARFZDISHUGS-MIXBDBMTSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)OC(=O)CCC(O)=O
OpenEye OEToolkits 1.6.1CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)OC(=O)CCC(=O)O)C)C
OpenEye OEToolkits 1.6.1CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)OC(=O)CCC(=O)O)C)C
CACTVS 3.352CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](CC[C]4(C)[CH]3CC[C]12C)OC(=O)CCC(O)=O
FormulaC31 H50 O4
NameCHOLESTEROL HEMISUCCINATE
ChEMBL
DrugBank
ZINCZINC000058638837
PDB chain8f0p Chain A Residue 1609 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8f0p Cryo-EM reveals an unprecedented binding site for Na V 1.7 inhibitors enabling rational design of potent hybrid inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		S332 G333 P390 W391 F1307
Binding residue
(residue number reindexed from 1)		S200 G201 P258 W259 F986
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8f0p, PDBe:8f0p, PDBj:8f0p
PDBsum8f0p
PubMed36975198
UniProtD0E0C2|SCNA1_PERAM Sodium channel protein PaFPC1;
Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

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