Structure of PDB 8xmm Chain A Binding Site BS08

Receptor Information

>8xmm Chain A (length=1145) Species: 9606 (Homo sapiens)

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 ID: LPE
• InChI: InChI=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
• InChIKey: XKBJVQHMEXMFDZ-AREMUKBSSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCCCCOCC(COP(=O)(O)OCC[N+](C)(C)C)O
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCCCCOC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)O
  ACDLabs 10.04: O=P(OCC(O)COCCCCCCCCCCCCCCCCCC)(OCC[N+](C)(C)C)O
  CACTVS 3.341: CCCCCCCCCCCCCCCCCCOC[C@@H](O)CO[P@](O)(=O)OCC[N+](C)(C)C
  CACTVS 3.341: CCCCCCCCCCCCCCCCCCOC[CH](O)CO[P](O)(=O)OCC[N+](C)(C)C
• Formula: C26 H57 N O6 P
• Name: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE;
  LPC-ETHER
• DrugBank: DB03633
• ZINC: ZINC000008860508
• PDB chain: 8xmm Chain A Residue 2017

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8xmm Dissection of the structure-function relationship of Na v channels.
• Resolution: 2.89 Å
• Binding residue (original residue number in PDB): W1178 R1182 Y1186 I1246 G1249 Y1250
• Binding residue (residue number reindexed from 1): W555 R559 Y563 I623 G626 Y627
• Annotation score: 1

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

External links

• PDB: RCSB:8xmm, PDBe:8xmm, PDBj:8xmm
• PDBsum: 8xmm
• PubMed: 38381792
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)