Structure of PDB 8fhd Chain A Binding Site BS03

Receptor Information
>8fhd Chain A (length=1294) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDSFKPFTPESLANIERRIAESKLKPKPNSDLEAGKSLPFIYGDIPQGLV
AVPLEDFDPYYLTQKTFVVLNRGKTLFRFSATPALYILSPFNLIRRIAIK
ILIHSVFSMIIMCTILTNCVFMTFSNPPDWSKNVEYTFTGIYTFESLVKI
IARGFCIDGFTFLRDPWNWLDFSVIMMAYITEFVNLGNVSALRTFRVLRA
LKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNL
RNKCVVWPINFNESYLENGTKGFDWEEYINNKTNFYTVPGMLEPLLCGNS
SDAGQCPEGYQCMKAGRNPNYGYTSFDTFSWAFLALFRLMTQDYWENLYQ
LTLRAAGKTYMIFFVLVIFVGSFYLVNLILAVVAMAYEEQNQATLEEAEQ
KEAEFKAMLEQLKKQQEPYWIKLKEIVNLIVMDPFVDLAITICIVLNTLF
MAMEHHPMTPQFEHVLAVGNLVFTGIFTAEMFLKLIAMDPYYYFQEGWNI
FDGFIVSLSLMELSLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIG
NSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINQDCELPRWHM
HDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVFMMVMVIGNLVVL
NLFLALLLSSFSADNLAATDDDGEMNNLQISVIRIKKGCQVNIEEGLGKS
WWILRKTCFLIVEHNWFETFIIFMILLSSGALAFEDIYIEQRKTIRTILE
YADKVFTYIFILEMLLKWTAYGFVKFFTNAWCWLDFLIVAVSLVSLIANA
LGYSELGAIKSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMNVLLV
CLIFWLIFSIMGVNLFAGKYHYCFNETSEIRFEIEDVNNKTECEKLMEGN
NTEIRWKNVKINFDNVGAGYLALLQVATFKGWMDIMYAAVDSRKPDEQPK
YEDNIYMYIYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTE
EQKKYYNAMKKLGSKKPQKPIPRPLNKIQGIVFDFVTQQAFDIVIMMLIC
LNMVTMMVETDTQSKQMENILYWINLVFVIFFTCECVLKMFALRHYYFTI
GWNIFDFVVVILSIVGMFLADIIEKYFVSPTLFRVIRLARIGRILRLIKG
AKGIRTLLFALMMSLPALFNIGLLLFLVMFIFSIFGMSNFAYVKHEAGID
DMFNFETFGNSMICLFQITTSAGWDGLLLPILNRPPDCSLDKEHPGSGFK
GDCGNPSVGIFFFVSYIIISFLIVVNMYIAIILENFSVATEESA
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 chain8fhd Chain A Residue 2006 [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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PDB8fhd Cryo-EM structure of human voltage-gated sodium channel Na v 1.6.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		S857 W858
Binding residue
(residue number reindexed from 1)		S538 W539
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:0005515 protein binding
GO:0031402 sodium ion binding
Biological Process
GO:0001508 action potential
GO:0006811 monoatomic ion transport
GO:0006814 sodium ion transport
GO:0007422 peripheral nervous system development
GO:0019228 neuronal action potential
GO:0021554 optic nerve development
GO:0034220 monoatomic ion transmembrane transport
GO:0035725 sodium ion transmembrane transport
GO:0042552 myelination
GO:0055085 transmembrane transport
GO:0086002 cardiac muscle cell action potential involved in contraction
Cellular Component
GO:0001518 voltage-gated sodium channel complex
GO:0002102 podosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030018 Z disc
GO:0030054 cell junction
GO:0030424 axon
GO:0031410 cytoplasmic vesicle
GO:0033268 node of Ranvier
GO:0034702 monoatomic ion channel complex
GO:0042995 cell projection
GO:0043194 axon initial segment
GO:0048787 presynaptic active zone membrane
GO:0070161 anchoring junction
GO:0098688 parallel fiber to Purkinje cell synapse
GO:0098839 postsynaptic density membrane
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8fhd, PDBe:8fhd, PDBj:8fhd
PDBsum8fhd
PubMed36696443
UniProtQ9UQD0|SCN8A_HUMAN Sodium channel protein type 8 subunit alpha (Gene Name=SCN8A)

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