Structure of PDB 8s9b Chain A Binding Site BS12

Receptor Information
>8s9b Chain A (length=1273) 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
RAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQPYW
IKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLLSVLR
SFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGM
QLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC
MEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDA
NNLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFE
SFIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKW
IAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRAL
RPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAG
KFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLG
YLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGS
FFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQK
PIPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTE
VLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFL
ADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALF
NIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQIT
TSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYII
ISFLVVVNMYIAVILENFSVATE
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 chain8s9b Chain A Residue 2016 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8s9b Structural mapping of Na v 1.7 antagonists.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		A1210 F1211 M1307 F1684
Binding residue
(residue number reindexed from 1)		A715 F716 M812 F1189
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:8s9b, PDBe:8s9b, PDBj:8s9b
PDBsum8s9b
PubMed37270609
UniProtQ15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

[Back to BioLiP]