Structure of PDB 8xmm Chain A Binding Site BS01

Receptor Information
>8xmm Chain A (length=1145) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLRRISIKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIY
TFESLVKILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNLGNVSAL
RTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIG
LQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDAL
LCGFSTDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYW
ENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANI
EEAKCSPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEE
FKNVLAIGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLV
ELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGAFGNLML
VLFIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVF
RVLCGEWIETMWDCMEVAGQAMCLIFYMMVFFIGNLVVLNLFLALLLSSF
SGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIERKKTIK
IILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTL
VANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMN
VLLVCLIFWLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFAL
MNVSQNVRWKNLKVNFDNVGLGYLSLLQVATFKGWTIIMYAAVDSVNVDK
QPKYEYSLYMYIYFIFFIIFGSFFTLNLFICVIIDNFNQQKKKLGGQDIF
MTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAFDISIMV
LICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYY
FTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRL
VKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKED
GINDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPKKVHPG
SSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIAVILENFSVATE
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 chain8xmm Chain A Residue 2003 [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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PDB8xmm Dissection of the structure-function relationship of Na v channels.
Resolution2.89 Å
Binding residue
(original residue number in PDB)		A762 H765 V1392
Binding residue
(residue number reindexed from 1)		A341 H344 V769
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:0006954 inflammatory response
GO:0007623 circadian rhythm
GO:0009636 response to toxic substance
GO:0009791 post-embryonic development
GO:0019228 neuronal action potential
GO:0019233 sensory perception of pain
GO:0034220 monoatomic ion transmembrane transport
GO:0035725 sodium ion transmembrane transport
GO:0048266 behavioral response to pain
GO:0050965 detection of temperature stimulus involved in sensory perception of pain
GO:0050974 detection of mechanical stimulus involved in sensory perception
GO:0055085 transmembrane transport
GO:0086002 cardiac muscle cell action potential involved in contraction
GO:0098870 action potential propagation
Cellular Component
GO:0001518 voltage-gated sodium channel complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030424 axon
GO:0033268 node of Ranvier
GO:0034702 monoatomic ion channel complex
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043679 axon terminus

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8xmm, PDBe:8xmm, PDBj:8xmm
PDBsum8xmm
PubMed38381792
UniProtQ15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

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