Structure of PDB 8xmm Chain A Binding Site BS03

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: 1PW
• InChI: InChI=1S/C20H40NO6P/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-20(23)19(21-18(2)22)17-27-28(24,25)26/h15-16,19-20,23H,3-14,17H2,1-2H3,(H,21,22)(H2,24,25,26)/b16-15+/t19-,20+/m0/s1
• InChIKey: HWPZKJVGDYNEAW-QUDYQQOWSA-N
• SMILES:
  CACTVS 3.370: CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[P](O)(O)=O)NC(C)=O
  CACTVS 3.370: CCCCCCCCCCCCCC=C[CH](O)[CH](CO[P](O)(O)=O)NC(C)=O
  OpenEye OEToolkits 1.7.6: CCCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)(O)O)NC(=O)C)O
  ACDLabs 12.01: O=C(NC(COP(=O)(O)O)C(O)/C=C/CCCCCCCCCCCCC)C
  OpenEye OEToolkits 1.7.6: CCCCCCCCCCCCCC=CC(C(COP(=O)(O)O)NC(=O)C)O
• Formula: C20 H40 N O6 P
• Name: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
• ZINC: ZINC000056870937
• PDB chain: 8xmm Chain A Residue 2005

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): I1321 M1322 T1404 F1452 F1748
• Binding residue (residue number reindexed from 1): I698 M699 T781 F829 F1125
• 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)