Structure of PDB 8f0q Chain A Binding Site BS01

Receptor Information
>8f0q Chain A (length=1114) 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
ISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYSPTLFRVIRLARIG
RILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMH
IRDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDH
ELGYPGNCGSRALGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKE
GLTDDDYDMFFEVW
Ligand information
Ligand IDX7R
InChIInChI=1S/C25H29Cl2FN2O4S/c1-15(18-9-19(26)11-20(27)10-18)30-7-5-16(6-8-30)14-34-24-13-23(28)22(12-21(24)17-3-4-17)25(31)29-35(2,32)33/h9-13,15-17H,3-8,14H2,1-2H3,(H,29,31)/t15-/m0/s1
InChIKeySXOAHIZWCZOILH-HNNXBMFYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC(c1cc(Cl)cc(Cl)c1)N1CCC(COc2cc(F)c(cc2C2CC2)C(=O)NS(C)(=O)=O)CC1
OpenEye OEToolkits 2.0.7C[C@@H](c1cc(cc(c1)Cl)Cl)N2CCC(CC2)COc3cc(c(cc3C4CC4)C(=O)NS(=O)(=O)C)F
OpenEye OEToolkits 2.0.7CC(c1cc(cc(c1)Cl)Cl)N2CCC(CC2)COc3cc(c(cc3C4CC4)C(=O)NS(=O)(=O)C)F
CACTVS 3.385C[CH](N1CCC(CC1)COc2cc(F)c(cc2C3CC3)C(=O)N[S](C)(=O)=O)c4cc(Cl)cc(Cl)c4
CACTVS 3.385C[C@H](N1CCC(CC1)COc2cc(F)c(cc2C3CC3)C(=O)N[S](C)(=O)=O)c4cc(Cl)cc(Cl)c4
FormulaC25 H29 Cl2 F N2 O4 S
Name5-cyclopropyl-4-({1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl}methoxy)-2-fluoro-N-(methanesulfonyl)benzamide
ChEMBLCHEMBL5094715
DrugBank
ZINC
PDB chain8f0q Chain A Residue 1604 [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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PDB8f0q Cryo-EM reveals an unprecedented binding site for Na V 1.7 inhibitors enabling rational design of potent hybrid inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N1206 G1247 A1251 I1267 R1268 R1271 R1274
Binding residue
(residue number reindexed from 1)		N885 G926 A930 I944 R945 R948 R951
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
View graph for
Cellular Component
External links
PDB RCSB:8f0q, PDBe:8f0q, PDBj:8f0q
PDBsum8f0q
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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