Structure of PDB 8xmn Chain A Binding Site BS03

Receptor Information
>8xmn Chain A (length=1277) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNNVSALRTFRVLRA
LKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNL
KHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDS
GQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTL
RAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKEL
EPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVL
AIGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLL
SVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGAFGNLTLVLAIIVFIFA
VVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIET
MWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEE
DPDANNLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEH
SWFESFIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEM
LLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRT
LRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVN
LFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDN
VGLGYLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFI
IFGSFFTLNLFICVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSK
KPQKPIPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQ
HMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIV
GMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSL
PALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICL
FQITTSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFV
SYIIISFLVVVNMYIAVILENFSVATE
Ligand information
Ligand IDLPE
InChIInChI=1S/C26H56NO6P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-22-31-24-26(28)25-33-34(29,30)32-23-21-27(2,3)4/h26,28H,5-25H2,1-4H3/p+1/t26-/m1/s1
InChIKeyXKBJVQHMEXMFDZ-AREMUKBSSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCOCC(COP(=O)(O)OCC[N+](C)(C)C)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCCCCCCCCOC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)O
ACDLabs 10.04O=P(OCC(O)COCCCCCCCCCCCCCCCCCC)(OCC[N+](C)(C)C)O
CACTVS 3.341CCCCCCCCCCCCCCCCCCOC[C@@H](O)CO[P@](O)(=O)OCC[N+](C)(C)C
CACTVS 3.341CCCCCCCCCCCCCCCCCCOC[CH](O)CO[P](O)(=O)OCC[N+](C)(C)C
FormulaC26 H57 N O6 P
Name1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE;
LPC-ETHER
ChEMBL
DrugBankDB03633
ZINCZINC000008860508
PDB chain8xmn Chain A Residue 2010 [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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PDB8xmn Dissection of the structure-function relationship of Na v channels.
Resolution3.37 Å
Binding residue
(original residue number in PDB)		S1206 A1210 F1211 K1219 F1652 F1656 F1684
Binding residue
(residue number reindexed from 1)		S715 A719 F720 K728 F1161 F1165 F1193
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:8xmn, PDBe:8xmn, PDBj:8xmn
PDBsum8xmn
PubMed38381792
UniProtQ15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

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