Structure of PDB 7wfr Chain A Binding Site BS09

Receptor Information
>7wfr Chain A (length=1100) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SWFSLFITVTILVNCVCMTRTDLPEKIEYVFTVIYTFEALIKILARGDPW
NWLDFSVITLAYVGTAIDLRGISGLRTFRVLRALKTVSVIPGLKVIVGAL
IHSVKKLADVTILTIFCLSVFALVGLQLFKGNLKNKCVKNDMAYSSHRKP
DIYINKRGTSDPLLCGNGSDSGHCPDGYICLKTSDNPDFNYTSFDSFAWA
FLSLFRLMTQDSWERLYQQTLRTSGKIYMIFFVLVIFLGSFYLVNLILAV
VTMAYEEQNQATWVKLKTILFGLVTDPFAELTITLCIVVNTIFMAMEHHG
MSPTFEAMLQIGNIVFTIFFTAEMVFKIIAFDPYYYFQKKWNIFDCIIVT
VSLLELGVAKKGSLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALG
NLTIILAIIVFVFALVGKQLLGENYRNNRKNISAPHEDWPRWHMHDFFHS
FLIVFRILCGEWIENMWACMEVGQKSICLILFLTVMVLGNLVVLNLFIAL
LLNSFFADVGWQVRKTCYRIVEHSWFESFIIFMILLSSGSLAFEDYYLDQ
KPTVKALLEYTDRVFTFIFVFEMLLKWVAYGFKKYFTNAWCWLDFLIVNI
SLISLTAKILEYSEVAPIKALRTLRALRPLRALSRFEGMRVVVDALVGAI
PSIMNVLLVCLIFWLIFSIMGVNLFAGKFWRCINYTDGEFSLVPLSIVNN
KSDCKIQNSTGSFFWVNVKVNFDNVAMGYLALLQVATFKGWMDIMYAAVD
SREVNMQPKWEDNVYMYLYFVIFIIFGGFFTLNLFVGVIIDNFNQQKKKL
GGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKFQGFVFDIVTRQAF
DITIMVLICLNMITMMVETDDQSEEKTKILGKINQFFVAVFTGECVMKMF
ALRQYYFTNGWNVFDFIVVVLSIASLIFSAILKSLQSYFSPTLFRVIRLA
RIGRILRLIRAAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMSS
FPHVRWEAGIDDMFNFQTFANSMLCLFQITTSAGWDGLLSPILNTGPPYC
DPNLPNSNGTRGDCGSPAVGIIFFTTYIIISFLIMVNMYIAVILENFNVA
Ligand information
Ligand IDCLR
InChIInChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
InChIKeyHVYWMOMLDIMFJA-DPAQBDIFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
CACTVS 3.341CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
ACDLabs 10.04OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
OpenEye OEToolkits 1.5.0CC(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)O)C)C
CACTVS 3.341CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
FormulaC27 H46 O
NameCHOLESTEROL
ChEMBLCHEMBL112570
DrugBankDB04540
ZINCZINC000003875383
PDB chain7wfr Chain A Residue 2027 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7wfr Structural basis for high-voltage activation and subtype-specific inhibition of human Na v 1.8.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		S341 V1495
Binding residue
(residue number reindexed from 1)		S196 V867
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
GO:0005272 sodium channel activity
GO:0044325 transmembrane transporter binding
GO:0099508 voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
Biological Process
GO:0002027 regulation of heart rate
GO:0006811 monoatomic ion transport
GO:0006814 sodium ion transport
GO:0007600 sensory perception
GO:0034220 monoatomic ion transmembrane transport
GO:0034765 regulation of monoatomic ion transmembrane transport
GO:0035725 sodium ion transmembrane transport
GO:0042475 odontogenesis of dentin-containing tooth
GO:0055085 transmembrane transport
GO:0055117 regulation of cardiac muscle contraction
GO:0060371 regulation of atrial cardiac muscle cell membrane depolarization
GO:0086002 cardiac muscle cell action potential involved in contraction
GO:0086010 membrane depolarization during action potential
GO:0086016 AV node cell action potential
GO:0086043 bundle of His cell action potential
GO:0099505 regulation of presynaptic membrane potential
Cellular Component
GO:0001518 voltage-gated sodium channel complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030424 axon
GO:0034702 monoatomic ion channel complex
GO:0042734 presynaptic membrane
GO:0070062 extracellular exosome
GO:0071439 clathrin complex
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7wfr, PDBe:7wfr, PDBj:7wfr
PDBsum7wfr
PubMed35858452
UniProtQ9Y5Y9|SCNAA_HUMAN Sodium channel protein type 10 subunit alpha (Gene Name=SCN10A)

[Back to BioLiP]