Structure of PDB 7w9k Chain A Binding Site BS12

Receptor Information
>7w9k Chain A (length=1413) 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
RAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKEL
EFQQMLDRLKKEQEPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAM
EHHPMTEEFKNVLAIGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDS
LIVTLSLVELFLLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGN
LTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFL
IVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLL
SSFSSDNLTAIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFGKIW
WNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIERKKTIKIILEY
ADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTL
GYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVC
LIFWLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQ
NVRWKNLKVNFDNVGLGYLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYE
YSLYMYIYFVVFIIFGSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQ
KKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAFDISIMVLICLN
MVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGW
NIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAK
GIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDM
FNFETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEG
DCGNPSVGIFYFVSYIIISFLVVVNMYIAVILENFSVATEESTEPLSEDD
FEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAMDL
PMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSYE
PITTTLKRKQEDV
Ligand information
Ligand IDP5S
InChIInChI=1S/C42H82NO10P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(44)50-35-38(36-51-54(48,49)52-37-39(43)42(46)47)53-41(45)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h38-39H,3-37,43H2,1-2H3,(H,46,47)(H,48,49)/t38-,39+/m1/s1
InChIKeyTZCPCKNHXULUIY-RGULYWFUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCCCCCCCCCCCC
ACDLabs 12.01O=C(OC(COP(=O)(OCC(C(=O)O)N)O)COC(=O)CCCCCCCCCCCCCCCCC)CCCCCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC
FormulaC42 H82 N O10 P
NameO-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine;
phosphatidyl serine
ChEMBLCHEMBL4297669
DrugBankDB00144
ZINCZINC000085588270
PDB chain7w9k Chain A Residue 2019 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7w9k High-resolution structures of human Na v 1.7 reveal gating modulation through alpha-pi helical transition of S6 IV.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G1489 W1578 F1581 R1631 L1634
Binding residue
(residue number reindexed from 1)		G1011 W1100 F1103 R1153 L1156
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:7w9k, PDBe:7w9k, PDBj:7w9k
PDBsum7w9k
PubMed35476982
UniProtQ15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

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