Structure of PDB 8xmn Chain A Binding Site BS01

Receptor Information

>8xmn Chain A (length=1277) Species: 9606 (Homo sapiens)

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 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: 8xmn Chain A Residue 2004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8xmn Dissection of the structure-function relationship of Na v channels.
• Resolution: 3.37 Å
• Binding residue (original residue number in PDB): P1733 S1734
• Binding residue (residue number reindexed from 1): P1242 S1243
• 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:8xmn, PDBe:8xmn, PDBj:8xmn
• PDBsum: 8xmn
• PubMed: 38381792
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)