Structure of PDB 8thh Chain A Binding Site BS06

Receptor Information

>8thh Chain A (length=1273) Species: 9606 (Homo sapiens)

GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNNVSALRTFRVLRA
LKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNL
KHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDS
GQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTL
RAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQPYW
IKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLLSVLR
SFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGM
QLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC
MEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDA
NNLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFE
SFIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKW
IAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRAL
RPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAG
KFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLG
YLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGS
FFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQK
PIPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTE
VLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFL
ADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALF
NIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQIT
TSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYII
ISFLVVVNMYIAVILENFSVATE

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: 8thh Chain A Residue 2008

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8thh Dual-pocket inhibition of Na v channels by the antiepileptic drug lamotrigine.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): P1733 I1737 F1738 S1742 I1745
• Binding residue (residue number reindexed from 1): P1238 I1242 F1243 S1247 I1250
• 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:8thh, PDBe:8thh, PDBj:8thh
• PDBsum: 8thh
• PubMed: 37782796
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)