Structure of PDB 8i5b Chain A Binding Site BS13

Receptor Information
>8i5b Chain A (length=1272) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNVSALRTFRVLRAL
KTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLK
HKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDSG
QCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLR
AAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQPYWI
KFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNL
VFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLLSVLRS
FRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQ
LFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCM
EVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDAN
NLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFES
FIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKWI
AYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALR
PLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGK
FYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGY
LSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGSF
FTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKP
IPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEV
LYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLA
DLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALFN
IGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITT
SAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIII
SFLVVVNMYIAVILENFSVATE
Ligand information
Ligand IDOJ0
InChIInChI=1S/C18H28N2O/c1-4-5-12-20-13-7-6-11-16(20)18(21)19-17-14(2)9-8-10-15(17)3/h8-10,16H,4-7,11-13H2,1-3H3,(H,19,21)/t16-/m0/s1
InChIKeyLEBVLXFERQHONN-INIZCTEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCN1CCCC[C@H]1C(=O)Nc2c(cccc2C)C
CACTVS 3.385CCCCN1CCCC[CH]1C(=O)Nc2c(C)cccc2C
CACTVS 3.385CCCCN1CCCC[C@H]1C(=O)Nc2c(C)cccc2C
OpenEye OEToolkits 2.0.7CCCCN1CCCCC1C(=O)Nc2c(cccc2C)C
FormulaC18 H28 N2 O
NameLevobupivacaine;
(2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)piperidine-2-carboxamide
ChEMBLCHEMBL1201193
DrugBankDB01002
ZINCZINC000001530812
PDB chain8i5b Chain A Residue 2021 [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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PDB8i5b Structural mapping of Na v 1.7 antagonists.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L968 I1457 D1458 L1760
Binding residue
(residue number reindexed from 1)		L632 I961 D962 L1264
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8i5b, PDBe:8i5b, PDBj:8i5b
PDBsum8i5b
PubMed37270609
UniProtQ15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)

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