Structure of PDB 8f0s Chain A Binding Site BS01

Receptor Information
>8f0s Chain A (length=1113) Species: 6978,9606 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTI
EVVVKVLARGFILHPFAYLRDPWNWLDFLVTLIGYITLVVYALRAFRVLR
SWRTVTIVPGWRTIVDALSLSITSLKDLVLLLLFSLSVFALIGLQLFMGN
LKHKCVKHFPADGSWGNFTDERWFNYTSNSSHWYIPDDWIEYPLCGNSSG
AGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFLSVFRLVTLDYWEDLYQL
ALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRADEEKVVL
SPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYIFTSIYIVEAV
LKIIALSPKFYFKDSWNVFDFIIVVFAILELGLVFRSFRLLRVFRLAKFW
PTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMERF
PDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAV
FFVGNLVILNLLIALLLNNYGWSNIRRVCFLLAKNKYFQKFVTAVLVITS
VLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKYFTS
KWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQV
VTSTLVEAVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLS
HEITMDRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDA
IDSREVHKQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRR
KAEGLSATDSRTQLIYRRAVMRTMSAKPVKRIPKNKIQGCIFDLVTNQAF
DISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLI
SLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYSPTLFRVIRLARIGR
ILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHI
RDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHE
LGYPGNCGSRALGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEG
LTDDDYDMFFEVW
Ligand information
Ligand IDX80
InChIInChI=1S/C27H34ClF2N3O4S/c1-33(2)24-10-6-5-9-23(24)31-18-11-12-26(22(30)13-18)38(35,36)32-27(34)19-14-20(28)25(15-21(19)29)37-16-17-7-3-4-8-17/h11-15,17,23-24,31H,3-10,16H2,1-2H3,(H,32,34)/t23-,24-/m0/s1
InChIKeyONUSAXHNRAIZSE-ZEQRLZLVSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CN(C)C1CCCCC1Nc1ccc(c(F)c1)S(=O)(=O)NC(=O)c1cc(Cl)c(OCC2CCCC2)cc1F
OpenEye OEToolkits 2.0.7CN(C)[C@H]1CCCC[C@@H]1Nc2ccc(c(c2)F)S(=O)(=O)NC(=O)c3cc(c(cc3F)OCC4CCCC4)Cl
OpenEye OEToolkits 2.0.7CN(C)C1CCCCC1Nc2ccc(c(c2)F)S(=O)(=O)NC(=O)c3cc(c(cc3F)OCC4CCCC4)Cl
CACTVS 3.385CN(C)[C@H]1CCCC[C@@H]1Nc2ccc(c(F)c2)[S](=O)(=O)NC(=O)c3cc(Cl)c(OCC4CCCC4)cc3F
CACTVS 3.385CN(C)[CH]1CCCC[CH]1Nc2ccc(c(F)c2)[S](=O)(=O)NC(=O)c3cc(Cl)c(OCC4CCCC4)cc3F
FormulaC27 H34 Cl F2 N3 O4 S
Name5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide
ChEMBL
DrugBank
ZINC
PDB chain8f0s Chain A Residue 1605 [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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PDB8f0s Cryo-EM reveals an unprecedented binding site for Na V 1.7 inhibitors enabling rational design of potent hybrid inhibitors.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		Y1203 W1204 N1206 I1243 G1247 M1248 I1267 R1268 R1271 R1274
Binding residue
(residue number reindexed from 1)		Y881 W882 N884 I921 G925 M926 I943 R944 R947 R950
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
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Biological Process
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Cellular Component
External links
PDB RCSB:8f0s, PDBe:8f0s, PDBj:8f0s
PDBsum8f0s
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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