Structure of PDB 6agf Chain A Binding Site BS05

Receptor Information
>6agf Chain A (length=1138) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVRRGAIKVLIHALFSMFIMITILTNCVFMTMSDPPPWSKNVEYTFTGIY
TFESLIKILARGFCVDDFTFLRDPWNWLDFSVIMMAYLTEFVDLGNISAL
RTFRVLRALKTITVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALVG
LQLFMGNLRQKCVRWPPPFDWDAYISDEGNFYFLEGSNDALLCGNSSDAG
HCPEGYECIKTGRNPNYGYTSYDTFSWAFLALFRLMTQDYWENLFQLTLR
AAGKTYMIFFVVIIFLGSFYLINLILAVVAMAYAEQNEATLAEDKENCCA
PWLKFKNIIHLIVMDPFVDLGITICIVLNTLFMAMEHYPMTEHFDNVLTV
GNLVFTGIFTAEMVLKLIAMDPYEYFQQGWNIFDSIIVTLSLVELGLANV
QGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVF
IFAVVGMQLFGKSYKECVCKIALDCNLPRWHMHDFFHSFLIVFRILCGEW
IETMWDCMEVAGQAMCLTVFLMVMVIGNLVVLNLFLALLLSSFSGKKWWT
LRRACFKIVEHNWFETFIVFMILLSSGALAFEDIYIEQRRVIRTILEYAD
KVFTYIFIMEMLLKWVAYGFKVYFTNAWCWLDFLIVDVSIISLVANWLGY
SELGPIKSLRTLRALRPLRALSRFEGMRVVVNALLGAIPSIMNVLLVCLI
FWLIFSIMGVNLFAGKFYYCINTTTSERFDISEVNNKSECESLMHTGQVR
WLNVKVNYDNVGLGYLSLLQVATFKGWMDIMYAAVDSREKEEQPQYEVNL
YMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKLGGKDIFMTEEQKKY
YNAMKKLGSKKPQKPIPRPQNKIQGMVYDLVTKQAFDITIMILICLNMVT
MMVETDNQSQLKVDILYNINMIFIIIFTGECVLKMLALRQYYFTVGWNIF
DFVVVILSIVGLALSDLIQKYFVSPTLFRVIRLARIGRVLRLIRGAKGIR
TLLFALMMSLPALFNIGLLLFLVMFIYSIFGMSNFAYVKKESGIDDMFNF
ETFGNSIICLFEITTSAGWDGLLNPILNSGPPDCDPNLENPGTSVKGDCG
NPSIGICFFCSYIIISFLIVVNMYIAIILENFNVATEE
Ligand information
Ligand ID9Z9
InChIInChI=1S/C34H56O5/c1-22-9-15-34(38-19-22)23(2)31-30(39-34)18-29-27-8-7-25-17-26(37-16-12-24(20-35-5)21-36-6)10-13-32(25,3)28(27)11-14-33(29,31)4/h7,22-24,26-31H,8-21H2,1-6H3/t22-,23+,26+,27-,28+,29+,30+,31+,32+,33+,34-/m1/s1
InChIKeyCEEBZAXXSRFQIC-GZSGZGDASA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC34C2C(OC1(OCC(CC1)C)C2C)CC3C5C(CC4)C6(C)C(=CC5)CC(CC6)OCCC(COC)COC
OpenEye OEToolkits 2.0.6C[C@@H]1CC[C@@]2([C@H]([C@H]3[C@@H](O2)C[C@@H]4[C@@]3(CC[C@H]5[C@H]4CC=C6[C@@]5(CC[C@@H](C6)OCCC(COC)COC)C)C)C)OC1
CACTVS 3.385COCC(CCO[CH]1CC[C]2(C)[CH]3CC[C]4(C)[CH](C[CH]5O[C]6(CC[CH](C)CO6)[CH](C)[CH]45)[CH]3CC=C2C1)COC
OpenEye OEToolkits 2.0.6CC1CCC2(C(C3C(O2)CC4C3(CCC5C4CC=C6C5(CCC(C6)OCCC(COC)COC)C)C)C)OC1
CACTVS 3.385COCC(CCO[C@H]1CC[C@]2(C)[C@H]3CC[C@@]4(C)[C@@H](C[C@@H]5O[C@]6(CC[C@@H](C)CO6)[C@@H](C)[C@H]45)[C@@H]3CC=C2C1)COC
FormulaC34 H56 O5
Name(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
ChEMBL
DrugBank
ZINC
PDB chain6agf Chain A Residue 1914 [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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PDB6agf Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta 1.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		L443 I1597 F1601
Binding residue
(residue number reindexed from 1)		L276 I1128 F1132
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
Biological Process
GO:0006811 monoatomic ion transport
GO:0006814 sodium ion transport
GO:0006936 muscle contraction
GO:0034220 monoatomic ion transmembrane transport
GO:0035725 sodium ion transmembrane transport
GO:0055085 transmembrane transport
GO:0086002 cardiac muscle cell action potential involved in contraction
GO:0100001 regulation of skeletal muscle contraction by action potential
Cellular Component
GO:0001518 voltage-gated sodium channel complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0034702 monoatomic ion channel complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6agf, PDBe:6agf, PDBj:6agf
PDBsum6agf
PubMed30190309
UniProtP35499|SCN4A_HUMAN Sodium channel protein type 4 subunit alpha (Gene Name=SCN4A)

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