Structure of PDB 8gz2 Chain B Binding Site BS01

Receptor Information
>8gz2 Chain B (length=1174) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FSATPALYILSPFNLIRRIAIKILIHSVFSMIIMCTILTNCVFMTFSNPP
DWSKNVEYTFTGIYTFESLVKIIARGFCIDGFTFLRDPWNWLDFSVIMMA
YITEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVM
ILTVFCLSVFALIGLQLFMGNLRNKCVVWPINFNESYLENGTKGFDWEEY
INNKTNFYTVPGMLEPLLCGNSSDAGQCPEGYQCMKAGRNPNYGYTSFDT
FSWAFLALFRLMTQDYWENLYQLTLRAAGKTYMIFFVLVIFVGSFYLVNL
ILAVVAMAYEEQNQATLEEAEPCWYKFANTFLIWECHPYWIKLKEIVNLI
VMDPFVDLAITICIVLNTLFMAMEHHPMTPQFEHVLAVGNLVFTGIFTAE
MFLKLIAMDPYYYFQEGWNIFDGFIVSLSLMELSLADVEGLSVLRSFRLL
RVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGK
SYKECVCKINQDCELPRWHMHDFFHSFLIVFRVLCGEWIETMWDCMEVAG
QAMCLIVFMMVMVIGNLVVLNLFLALLLSSFSGKSWWILRKTCFLIVEHN
WFETFIIFMILLSSGALAFEDIYIEQRKTIRTILEYADKVFTYIFILEML
LKWTAYGFVKFFTNAWCWLDFLIVAVSLVSLIANALGYSELGAIKSLRTL
RALRPLRALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNL
FAGKYHYCFNETSEIRFEIEDVNNKTECEKLMEGNNTEIRWKNVKINFDN
VGAGYLALLQVATFKGWMDIMYAAVDSRKPDEQPKYEDNIYMYIYFVIFI
IFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSK
KPQKPIPRPLNKIQGIVFDFVTQQAFDIVIMMLICLNMVTMMVETDTQSK
QMENILYWINLVFVIFFTCECVLKMFALRHYYFTIGWNIFDFVVVILSIV
GMFLADIIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSL
PALFNIGLLLFLVMFIFSIFGMSNFAYVKHEAGIDDMFNFETFGNSMICL
FQITTSAGWDGLLLPILNRPPDCSLDKEHPGSGFKGDCGNPSVGIFFFVS
YIIISFLIVVNMYIAIILENFSVA
Ligand information
Ligand IDWMK
InChIInChI=1S/C11H15N3O7/c12-8-13-6-2-4-9(17,1-15)5-3(16)10(2,14-8)7(19-6)11(18,20-4)21-5/h2-7,15-18H,1H2,(H3,12,13,14)/t2-,3+,4-,5+,6+,7+,9+,10-,11+/m1/s1
InChIKeySTNXQECXKDMLJK-LQRXLWILSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C(C1(C2C3C4N=C(NC35C(C1OC(C5O4)(O2)O)O)N)O)O
CACTVS 3.385NC1=N[CH]2O[CH]3[C]4(O)O[CH]5[CH](O)[C]3(N1)[CH]2[CH](O4)[C]5(O)CO
ACDLabs 12.01NC=1NC23C(O)C4OC5(O)OC(C2C(OC35)N=1)C4(O)CO
OpenEye OEToolkits 2.0.7C([C@@]1([C@H]2[C@@H]3[C@H]4N=C(N[C@@]35[C@H]([C@@H]1O[C@]([C@H]5O4)(O2)O)O)N)O)O
CACTVS 3.385NC1=N[C@H]2O[C@@H]3[C@@]4(O)O[C@H]5[C@H](O)[C@]3(N1)[C@@H]2[C@@H](O4)[C@@]5(O)CO
FormulaC11 H15 N3 O7
Name(1R,2S,3S,4R,5R,9S,11S,12S,14R)-7-amino-2,4,12-trihydroxy-2-(hydroxymethyl)-10,13,15-trioxa-6,8-diazapentacyclo[7.4.1.1~3,12~.0~5,11~.0~5,14~]pentadec-7-en-8-ium (non-preferred name);
4,9-anhydro-tetrodotoxin
ChEMBL
DrugBank
ZINC
PDB chain8gz2 Chain B Residue 2002 [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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PDB8gz2 Structure of human Na V 1.6 channel reveals Na + selectivity and pore blockade by 4,9-anhydro-tetrodotoxin.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		Y371 E373 E936 E939 G1414 M1416 D1708
Binding residue
(residue number reindexed from 1)		Y266 E268 E537 E540 G816 M818 D1110
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8gz2, PDBe:8gz2, PDBj:8gz2
PDBsum8gz2
PubMed36823201
UniProtQ9UQD0|SCN8A_HUMAN Sodium channel protein type 8 subunit alpha (Gene Name=SCN8A)

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