Target Information
| Target General Information | Top | |||||
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| Target ID |
T76937
(Former ID: TTDR01255)
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| Target Name |
Voltage-gated sodium channel alpha Nav1.3 (SCN3A)
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| Synonyms |
Voltage-gated sodium channel subunit alpha Nav1.3; Voltage-gated sodium channel subtype III; Sodium channel protein, brain III subunit alpha; Sodium channel protein type III subunit alpha; Sodium channel protein type 3 subunit alpha; Sodium channel protein brain III subunit alpha; NAC3; KIAA1356
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| Gene Name |
SCN3A
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| Target Type |
Successful target
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[1] | ||||
| Disease | [+] 1 Target-related Diseases | + | ||||
| 1 | Angina pectoris [ICD-11: BA40] | |||||
| Function |
Assuming opened or closed conformations in response to the voltage difference across the membrane, forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. May contribute to the regulation of serotonin/5-hydroxytryptamine release by enterochromaffin cells. In pancreatic endocrine cells, required for both glucagon and glucose-induced insulin secretion. Mediates the voltage-dependent sodium ion permeability of excitable membranes.
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| BioChemical Class |
Voltage-gated ion channel
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| UniProt ID | ||||||
| Sequence |
MAQALLVPPGPESFRLFTRESLAAIEKRAAEEKAKKPKKEQDNDDENKPKPNSDLEAGKN
LPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVMNKGKAIFRFSATSALYILTPLNPVRKI AIKILVHSLFSMLIMCTILTNCVFMTLSNPPDWTKNVEYTFTGIYTFESLIKILARGFCL EDFTFLRDPWNWLDFSVIVMAYVTEFVSLGNVSALRTFRVLRALKTISVIPGLKTIVGAL IQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLRNKCLQWPPSDSAFETNTTSYFNGTMD SNGTFVNVTMSTFNWKDYIGDDSHFYVLDGQKDPLLCGNGSDAGQCPEGYICVKAGRNPN YGYTSFDTFSWAFLSLFRLMTQDYWENLYQLTLRAAGKTYMIFFVLVIFLGSFYLVNLIL AVVAMAYEEQNQATLEEAEQKEAEFQQMLEQLKKQQEEAQAVAAASAASRDFSGIGGLGE LLESSSEASKLSSKSAKEWRNRRKKRRQREHLEGNNKGERDSFPKSESEDSVKRSSFLFS MDGNRLTSDKKFCSPHQSLLSIRGSLFSPRRNSKTSIFSFRGRAKDVGSENDFADDEHST FEDSESRRDSLFVPHRHGERRNSNVSQASMSSRMVPGLPANGKMHSTVDCNGVVSLVGGP SALTSPTGQLPPEGTTTETEVRKRRLSSYQISMEMLEDSSGRQRAVSIASILTNTMEELE ESRQKCPPCWYRFANVFLIWDCCDAWLKVKHLVNLIVMDPFVDLAITICIVLNTLFMAME HYPMTEQFSSVLTVGNLVFTGIFTAEMVLKIIAMDPYYYFQEGWNIFDGIIVSLSLMELG LSNVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVG MQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMC LIVFMLVMVIGNLVVLNLFLALLLSSFSSDNLAATDDDNEMNNLQIAVGRMQKGIDYVKN KMRECFQKAFFRKPKVIEIHEGNKIDSCMSNNTGIEISKELNYLRDGNGTTSGVGTGSSV EKYVIDENDYMSFINNPSLTVTVPIAVGESDFENLNTEEFSSESELEESKEKLNATSSSE GSTVDVVLPREGEQAETEPEEDLKPEACFTEGCIKKFPFCQVSTEEGKGKIWWNLRKTCY SIVEHNWFETFIVFMILLSSGALAFEDIYIEQRKTIKTMLEYADKVFTYIFILEMLLKWV AYGFQTYFTNAWCWLDFLIVDVSLVSLVANALGYSELGAIKSLRTLRALRPLRALSRFEG MRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYHCVNMTTGNMFDISDVNN LSDCQALGKQARWKNVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRDVKLQPVYEE NLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLG SKKPQKPIPRPANKFQGMVFDFVTRQVFDISIMILICLNMVTMMVETDDQGKYMTLVLSR INLVFIVLFTGEFVLKLVSLRHYYFTIGWNIFDFVVVILSIVGMFLAEMIEKYFVSPTLF RVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYV KKEAGIDDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSAPPDCDPDTIHPGSSVKGD CGNPSVGIFFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDDFEMFYEVWEKF DPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRV LGESGEMDALRIQMEDRFMASNPSKVSYEPITTTLKRKQEEVSAAIIQRNFRCYLLKQRL KNISSNYNKEAIKGRIDLPIKQDMIIDKLNGNSTPEKTDGSSSTTSPPSYDSVTKPDKEK FEKDKPEKESKGKEVRENQK Click to Show/Hide
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| 3D Structure | Click to Show 3D Structure of This Target | AlphaFold | ||||
| Drugs and Modes of Action | Top | |||||
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| Approved Drug(s) | [+] 1 Approved Drugs | + | ||||
| 1 | LIDOFLAZINE | Drug Info | Approved | Angina pectoris | [2] | |
| Discontinued Drug(s) | [+] 1 Discontinued Drugs | + | ||||
| 1 | SIPATRIGINE | Drug Info | Discontinued in Phase 2 | Neurological disorder | [3] | |
| Mode of Action | [+] 4 Modes of Action | + | ||||
| Inhibitor | [+] 23 Inhibitor drugs | + | ||||
| 1 | LIDOFLAZINE | Drug Info | [1] | |||
| 2 | Aryl carboxamide derivative 1 | Drug Info | [4] | |||
| 3 | Aryl carboxamide derivative 2 | Drug Info | [4] | |||
| 4 | Pyrrolo-pyridinone derivative 5 | Drug Info | [4] | |||
| 5 | Pyrrolo-pyridinone derivative 6 | Drug Info | [4] | |||
| 6 | SIPATRIGINE | Drug Info | [5] | |||
| 7 | PD-85639 | Drug Info | [1] | |||
| 8 | U-92032 | Drug Info | [6] | |||
| 9 | 2-(1-Pentyl-hexyl)-4-phenyl-1H-imidazole | Drug Info | [7] | |||
| 10 | 2-Hexyl-4-(4-isobutyl-phenyl)-1H-imidazole | Drug Info | [7] | |||
| 11 | 2-Hydroxy-2-phenyl-nonanoic acid amide | Drug Info | [8] | |||
| 12 | 4-Biphenyl-4-yl-2-(1-pentyl-hexyl)-1H-imidazole | Drug Info | [7] | |||
| 13 | 4-Biphenyl-4-yl-2-(1-propyl-butyl)-1H-imidazole | Drug Info | [7] | |||
| 14 | 4-Biphenyl-4-yl-2-cyclohexylmethyl-1H-imidazole | Drug Info | [7] | |||
| 15 | 4-Biphenyl-4-yl-2-hexyl-1H-imidazole | Drug Info | [7] | |||
| 16 | 4-Biphenyl-4-yl-2-methyl-1H-imidazole | Drug Info | [7] | |||
| 17 | 5-Ethyl-3-methyl-5-phenyl-oxazolidine-2,4-dione | Drug Info | [9] | |||
| 18 | 5-Heptyl-5-phenyl-imidazolidine-2,4-dione | Drug Info | [8] | |||
| 19 | 5-Hexyl-5-phenyl-imidazolidine-2,4-dione | Drug Info | [8] | |||
| 20 | 5-Nonyl-5-phenyl-imidazolidine-2,4-dione | Drug Info | [8] | |||
| 21 | BW-202W92 | Drug Info | [11] | |||
| 22 | CCNCSSKWCRDHSRCC | Drug Info | [12] | |||
| 23 | L-741742 | Drug Info | [13] | |||
| Blocker | [+] 1 Blocker drugs | + | ||||
| 1 | Pyrimidine derivative 1 | Drug Info | [4] | |||
| Activator | [+] 2 Activator drugs | + | ||||
| 1 | batrachotoxin | Drug Info | [10] | |||
| 2 | veratridine | Drug Info | [10] | |||
| Antagonist | [+] 1 Antagonist drugs | + | ||||
| 1 | RQ-00203066 | Drug Info | [10] | |||
| Cell-based Target Expression Variations | Top | |||||
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| Cell-based Target Expression Variations | ||||||
| Drug Binding Sites of Target | Top | |||||
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| Ligand Name: Bulleyaconitine A | Ligand Info | |||||
| Structure Description | cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA | PDB:7W77 | ||||
| Method | Electron microscopy | Resolution | 3.30 Å | Mutation | No | [14] |
| PDB Sequence |
PVRKIAIKIL
125 VHSLFSMLIM135 CTILTNCVFM145 TLSNPPDWTK155 NVEYTFTGIY165 TFESLIKILA 175 RGFCLEDFTF185 LRDPWNWLDF195 SVIVMAYVTE205 FVSLVSALRT217 FRVLRALKTI 227 SVIPGLKTIV237 GALIQSVKKL247 SDVMILTVFC257 LSVFALIGLQ267 LFMGNLRNKC 277 LQWPPSFNWK316 DYIGDDSHFY326 VLDGQKDPLL336 CGNGSDAGQC346 PEGYICVKAG 356 RNPNYGYTSF366 DTFSWAFLSL376 FRLMTQDYWE386 NLYQLTLRAA396 GKTYMIFFVL 406 VIFLGSFYLV416 NLILAVVAMA426 YEEQNQATLE436 EADCCDAWLK748 VKHLVNLIVM 758 DPFVDLAITI768 CIVLNTLFMA778 MEHYPMTEQF788 SSVLTVGNLV798 FTGIFTAEMV 808 LKIIAMDPYY818 YFQEGWNIFD828 GIIVSLSLME838 LGLSNVEGLS848 VLRSFRLLRV 858 FKLAKSWPTL868 NMLIKIIGNS878 VGALGNLTLV888 LAIIVFIFAV898 VGMQLFGKSY 908 KECVCKINDD918 CTLPRWHMND928 FFHSFLIVFR938 VLCGEWIETM948 WDCMEVAGQT 958 MCLIVFMLVM968 VIGNLVVLNL978 FLALLLSSFG1189 KIWWNLRKTC1199 YSIVEHNWFE 1209 TFIVFMILLS1219 SGALAFEDIY1229 IEQRKTIKTM1239 LEYADKVFTY1249 IFILEMLLKW 1259 VAYGFQTYFT1269 NAWCWLDFLI1279 VDVSLVSLVA1289 NALGYSELGA1299 IKSLRTLRAL 1309 RPLRALSRFE1319 GMRVVVNALV1329 GAIPSIMNVL1339 LVCLIFWLIF1349 SIMGVNLFAG 1359 KFYHCVNMTT1369 GNMFDISDVN1379 NLSDCQALGK1389 QARWKNVKVN1399 FDNVGAGYLA 1409 LLQVATFKGW1419 MDIMYAAVDS1429 RDVKLQPVYE1439 ENLYMYLYFV1449 IFIIFGSFFT 1459 LNLFIGVIID1469 NFNQQKKKFG1479 GQDIFMTEEQ1489 KKYYNAMKKL1499 GSKKPQKPIP 1509 RPANKFQGMV1519 FDFVTRQVFD1529 ISIMILICLN1539 MVTMMVETDD1549 QGKYMTLVLS 1559 RINLVFIVLF1569 TGEFVLKLVS1579 LRHYYFTIGW1589 NIFDFVVVIL1599 SIVGMFLAEM 1609 IEKYFVSPTL1619 FRVIRLARIG1629 RILRLIKGAK1639 GIRTLLFALM1649 MSLPALFNIG 1659 LLLFLVMFIY1669 AIFGMSNFAY1679 VKKEAGIDDM1689 FNFETFGNSM1699 ICLFQITTSA 1709 GWDGLLAPIL1719 NSAPPDCDPD1729 TIHPGSSVKG1739 DCGNPSVGIF1749 FFVSYIIISF 1759 LVVVNMYIAV1769 ILENFSVAT
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MET251
4.743
THR254
4.556
PHE377
3.896
MET380
3.578
THR381
2.614
GLN382
4.248
ASP383
4.521
SER412
3.690
VAL416
1.491
ILE419
3.786
LEU420
3.624
VAL939
4.415
LEU940
3.594
CYS941
2.779
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| Ligand Name: 2,2-diphenyl-N-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]acetamide | Ligand Info | |||||
| Structure Description | Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431 | PDB:7W7F | ||||
| Method | Electron microscopy | Resolution | 3.35 Å | Mutation | No | [14] |
| PDB Sequence |
PVRKIAIKIL
125 VHSLFSMLIM135 CTILTNCVFM145 TLSNPPDWTK155 NVEYTFTGIY165 TFESLIKILA 175 RGFCLEDFTF185 LRDPWNWLDF195 SVIVMAYVTE205 FVSLVSALRT217 FRVLRALKTI 227 SVIPGLKTIV237 GALIQSVKKL247 SDVMILTVFC257 LSVFALIGLQ267 LFMGNLRNKC 277 LQWPPSFNWK316 DYIGDDSHFY326 VLDGQKDPLL336 CGNGSDAGQC346 PEGYICVKAG 356 RNPNYGYTSF366 DTFSWAFLSL376 FRLMTQDYWE386 NLYQLTLRAA396 GKTYMIFFVL 406 VIFLGSFYLV416 NLILAVVAMA426 YEEQNQATLE436 EADCCDAWLK748 VKHLVNLIVM 758 DPFVDLAITI768 CIVLNTLFMA778 MEHYPMTEQF788 SSVLTVGNLV798 FTGIFTAEMV 808 LKIIAMDPYY818 YFQEGWNIFD828 GIIVSLSLME838 LGLSNVEGLS848 VLRSFRLLRV 858 FKLAKSWPTL868 NMLIKIIGNS878 VGALGNLTLV888 LAIIVFIFAV898 VGMQLFGKSY 908 KECVCKINDD918 CTLPRWHMND928 FFHSFLIVFR938 VLCGEWIETM948 WDCMEVAGQT 958 MCLIVFMLVM968 VIGNLVVLNL978 FLALLLSSFG1189 KIWWNLRKTC1199 YSIVEHNWFE 1209 TFIVFMILLS1219 SGALAFEDIY1229 IEQRKTIKTM1239 LEYADKVFTY1249 IFILEMLLKW 1259 VAYGFQTYFT1269 NAWCWLDFLI1279 VDVSLVSLVA1289 NALGYSELGA1299 IKSLRTLRAL 1309 RPLRALSRFE1319 GMRVVVNALV1329 GAIPSIMNVL1339 LVCLIFWLIF1349 SIMGVNLFAG 1359 KFYHCVNMTT1369 GNMFDISDVN1379 NLSDCQALGK1389 QARWKNVKVN1399 FDNVGAGYLA 1409 LLQVATFKGW1419 MDIMYAAVDS1429 RDVKLQPVYE1439 ENLYMYLYFV1449 IFIIFGSFFT 1459 LNLFIGVIID1469 NFNQQKKKFG1479 GQDIFMTEEQ1489 KKYYNAMKKL1499 GSKKPQKPIP 1509 RPANKFQGMV1519 FDFVTRQVFD1529 ISIMILICLN1539 MVTMMVETDD1549 QGKYMTLVLS 1559 RINLVFIVLF1569 TGEFVLKLVS1579 LRHYYFTIGW1589 NIFDFVVVIL1599 SIVGMFLAEM 1609 IEKYFVSPTL1619 FRVIRLARIG1629 RILRLIKGAK1639 GIRTLLFALM1649 MSLPALFNIG 1659 LLLFLVMFIY1669 AIFGMSNFAY1679 VKKEAGIDDM1689 FNFETFGNSM1699 ICLFQITTSA 1709 GWDGLLAPIL1719 NSAPPDCDPD1729 TIHPGSSVKG1739 DCGNPSVGIF1749 FFVSYIIISF 1759 LVVVNMYIAV1769 ILENFSVAT
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| Click to View More Binding Site Information of This Target with Different Ligands | ||||||
| Different Human System Profiles of Target | Top |
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Human Similarity Proteins
of target is determined by comparing the sequence similarity of all human proteins with the target based on BLAST. The similarity proteins for a target are defined as the proteins with E-value < 0.005 and outside the protein families of the target.
A target that has fewer human similarity proteins outside its family is commonly regarded to possess a greater capacity to avoid undesired interactions and thus increase the possibility of finding successful drugs
(Brief Bioinform, 21: 649-662, 2020).
Human Pathway Affiliation
of target is determined by the life-essential pathways provided on KEGG database. The target-affiliated pathways were defined based on the following two criteria (a) the pathways of the studied target should be life-essential for both healthy individuals and patients, and (b) the studied target should occupy an upstream position in the pathways and therefore had the ability to regulate biological function.
Targets involved in a fewer pathways have greater likelihood to be successfully developed, while those associated with more human pathways increase the chance of undesirable interferences with other human processes
(Pharmacol Rev, 58: 259-279, 2006).
Biological Network Descriptors
of target is determined based on a human protein-protein interactions (PPI) network consisting of 9,309 proteins and 52,713 PPIs, which were with a high confidence score of ≥ 0.95 collected from STRING database.
The network properties of targets based on protein-protein interactions (PPIs) have been widely adopted for the assessment of target’s druggability. Proteins with high node degree tend to have a high impact on network function through multiple interactions, while proteins with high betweenness centrality are regarded to be central for communication in interaction networks and regulate the flow of signaling information
(Front Pharmacol, 9, 1245, 2018;
Curr Opin Struct Biol. 44:134-142, 2017).
Human Similarity Proteins
Human Pathway Affiliation
Biological Network Descriptors
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| Protein Name | Pfam ID | Percentage of Identity (%) | E value |
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| Sodium/hydrogen exchanger 11 (SLC9C2) | 26.515 (35/132) | 2.11E-04 |
| KEGG Pathway | Pathway ID | Affiliated Target | Pathway Map |
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| Taste transduction | hsa04742 | Affiliated Target |
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| Class: Organismal Systems => Sensory system | Pathway Hierarchy | ||
| Degree | 1 | Degree centrality | 1.07E-04 | Betweenness centrality | 0.00E+00 |
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| Closeness centrality | 1.31E-01 | Radiality | 1.11E+01 | Clustering coefficient | 0.00E+00 |
| Neighborhood connectivity | 3.00E+00 | Topological coefficient | 1.00E+00 | Eccentricity | 15 |
| Download | Click to Download the Full PPI Network of This Target | ||||
| Chemical Structure based Activity Landscape of Target | Top |
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| Drug Property Profile of Target | Top | |
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| (1) Molecular Weight (mw) based Drug Clustering | (2) Octanol/Water Partition Coefficient (xlogp) based Drug Clustering | |
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| (3) Hydrogen Bond Donor Count (hbonddonor) based Drug Clustering | (4) Hydrogen Bond Acceptor Count (hbondacc) based Drug Clustering | |
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| (5) Rotatable Bond Count (rotbonds) based Drug Clustering | (6) Topological Polar Surface Area (polararea) based Drug Clustering | |
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| "RO5" indicates the cutoff set by lipinski's rule of five; "D123AB" colored in GREEN denotes the no violation of any cutoff in lipinski's rule of five; "D123AB" colored in PURPLE refers to the violation of only one cutoff in lipinski's rule of five; "D123AB" colored in BLACK represents the violation of more than one cutoffs in lipinski's rule of five | ||
| Co-Targets | Top | |||||
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| Co-Targets | ||||||
| Target Poor or Non Binders | Top | |||||
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| Target Poor or Non Binders | ||||||
| Target Regulators | Top | |||||
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| Target-regulating microRNAs | ||||||
| Target Affiliated Biological Pathways | Top | |||||
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| Reactome | [+] 1 Reactome Pathways | + | ||||
| 1 | Interaction between L1 and Ankyrins | |||||
| Target-Related Models and Studies | Top | |||||
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| Target Validation | ||||||
| References | Top | |||||
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| REF 1 | Synthesis and pharmacological evaluation of phenylacetamides as sodium-channel blockers. J Med Chem. 1994 Jan 21;37(2):268-74. | |||||
| REF 2 | Drugs@FDA. U.S. Food and Drug Administration. U.S. Department of Health & Human Services. 2015 | |||||
| REF 3 | Trusted, scientifically sound profiles of drug programs, clinical trials, safety reports, and company deals, written by scientists. Springer. 2015. Adis Insight (drug id 800003904) | |||||
| REF 4 | Sodium channel blockers: a patent review (2010 - 2014).Expert Opin Ther Pat. 2015 Mar;25(3):279-90. | |||||
| REF 5 | Synthesis and structure-activity relationships of 6,7-benzomorphan derivatives as use-dependent sodium channel blockers for the treatment of stroke. J Med Chem. 2002 Aug 15;45(17):3755-64. | |||||
| REF 6 | Discovery of (2S)-1-(4-amino-2,3,5- trimethylphenoxy)-3-[4-[4-(4- fluorobenzyl)phenyl]-1-piperazinyl]-2-propanol dimethanesulfonate (SUN N8075): a ... J Med Chem. 2000 Sep 7;43(18):3372-6. | |||||
| REF 7 | 2-Alkyl-4-arylimidazoles: structurally novel sodium channel modulators. Bioorg Med Chem Lett. 2004 Jul 5;14(13):3521-3. | |||||
| REF 8 | Comparative molecular field analysis of hydantoin binding to the neuronal voltage-dependent sodium channel. J Med Chem. 1999 May 6;42(9):1537-45. | |||||
| REF 9 | Sodium channel binding and anticonvulsant activities for the enantiomers of a bicyclic 2,4-oxazolidinedione and monocyclic models. J Med Chem. 1989 Jul;32(7):1577-80. | |||||
| REF 10 | URL: http://www.guidetopharmacology.org Nucleic Acids Res. 2015 Oct 12. pii: gkv1037. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. (Target id: 580). | |||||
| REF 11 | Oxadiazolylindazole sodium channel modulators are neuroprotective toward hippocampal neurones. J Med Chem. 2009 May 14;52(9):2694-707. | |||||
| REF 12 | Structure/function characterization of micro-conotoxin KIIIA, an analgesic, nearly irreversible blocker of mammalian neuronal sodium channels. J Biol Chem. 2007 Oct 19;282(42):30699-706. | |||||
| REF 13 | 1-(3-Cyanobenzylpiperidin-4-yl)-5-methyl-4-phenyl-1, 3-dihydroimidazol-2-one: a selective high-affinity antagonist for the human dopamine D(4) rece... J Med Chem. 1999 Jul 15;42(14):2706-15. | |||||
| REF 14 | Structural basis for modulation of human Na(V)1.3 by clinical drug and selective antagonist. Nat Commun. 2022 Mar 11;13(1):1286. | |||||
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