Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T12119 | Target Info | |||
| Target Name | Voltage-gated sodium channel alpha Nav1.7 (SCN9A) | ||||
| Synonyms | hNE-Na; Voltage-gated sodium channel subunit alpha Nav1.7; Sodium channel proteintype IX subunit alpha; Sodium channel proteintype 9 subunit alpha; Sodium channel protein type IX subunit alpha; Sodium channel protein type 9 subunit alpha; Peripheral sodium channel 1; PN1; Neuroendocrine sodium channel; NENA | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | SCN9A | ||||
| Biochemical Class | Voltage-gated ion channel | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Tetrodotoxin | Ligand Info | |||
| Canonical SMILES | C(C1(C2C3C(N=C(NC34C(C1OC(C4O)(O2)O)O)N)O)O)O | ||||
| InChI | 1S/C11H17N3O8/c12-8-13-6(17)2-4-9(19,1-15)5-3(16)10(2,14-8)7(18)11(20,21-4)22-5/h2-7,15-20H,1H2,(H3,12,13,14)/t2-,3-,4-,5+,6-,7+,9+,10-,11+/m1/s1 | ||||
| InChIKey | CFMYXEVWODSLAX-QOZOJKKESA-N | ||||
| PubChem Compound ID | 11174599 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7W9M Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (S6IV pi helix conformer) | ||||||
| Method | Electron microscopy | Resolution | 3.00 Å | Mutation | Yes | [1] |
| PDB Sequence |
GPQSFVHFTK
17 QSLALIEQRI27 AERKSKEPKP49 SSDLEAGKQL59 PFIYGDIPPG69 MVSEPLEDLD 79 PYYADKKTFI89 VLNKGKTIFR99 FNATPALYML109 SPFSPLRRIS119 IKILVHSLFS 129 MLIMCTILTN139 CIFMTMNNPP149 DWTKNVEYTF159 TGIYTFESLV169 KILARGFCVG 179 EFTFLRDPWN189 WLDFVVIVFA199 YLTEFVNNVS211 ALRTFRVLRA221 LKTISVIPGL 231 KTIVGALIQS241 VKKLSDVMIL251 TVFCLSVFAL261 IGLQLFMGNL271 KHKCFRNSLE 281 NNETLESIMN291 TLESEEDFRK301 YFYYLEGSKD311 ALLCGFSTDS321 GQCPEGYTCV 331 KIGRNPDYGY341 TSFDTFSWAF351 LALFRLMTQD361 YWENLYQQTL371 RAAGKTYMIF 381 FVVVIFLGSF391 YLINLILAVV401 AMAYKEQNQA411 NIEEAKQKEL421 EFQQMLDRLK 431 KEQEPYWIKF733 KKCIYFIVMD743 PFVDLAITIC753 IVLNTLFMAM763 EHHPMTEEFK 773 NVLAIGNLVF783 TGIFAAEMVL793 KLIAMDPYEY803 FQVGWNIFDS813 LIVTLSLVEL 823 FLADVEGLSV833 LRSFRLLRVF843 KLAKSWPTLN853 MLIKIIGNSV863 GALGNLTLVL 873 AIIVFIFAVV883 GMQLFGKSYK893 ECVCKINDDC903 TLPRWHMNDF913 FHSFLIVFRV 923 LCGEWIETMW933 DCMEVAGQAM943 CLIVYMMVMV953 IGNLVVLNLF963 LALLLSSFSS 973 DNLTAIEEDP983 DANNLQIAVT993 RIKKGINYVK1003 QTLREFILKA1013 FGKIWWNIRK 1183 TCYKIVEHSW1193 FESFIVLMIL1203 LSSGALAFED1213 IYIERKKTIK1223 IILEYADKIF 1233 TYIFILEMLL1243 KWIAYGYKTY1253 FTNAWCWLDF1263 LIVDVSLVTL1273 VANTLGYSDL 1283 GPIKSLRTLR1293 ALRPLRALSR1303 FEGMRVVVNA1313 LIGAIPSIMN1323 VLLVCLIFWL 1333 IFSIMGVNLF1343 AGKFYECINT1353 TDGSRFPASQ1363 VPNRSECFAL1373 MNVSQNVRWK 1383 NLKVNFDNVG1393 LGYLSLLQVA1403 TFKGWTIIMY1413 AAVDSVNVDK1423 QPKYEYSLYM 1433 YIYFVVFIIF1443 GSFFTLNLFI1453 GVIIDNFNQQ1463 KKKLGGQDIF1473 MTEEQKKYYN 1483 AMKKLGSKKP1493 QKPIPRPGNK1503 IQGCIFDLVT1513 NQAFDISIMV1523 LICLNMVTMM 1533 VEKEGQSQHM1543 TEVLYWINVV1553 FIILFTGECV1563 LKLISLRHYY1573 FTVGWNIFDF 1583 VVVIISIVGM1593 FLADLIETYF1603 VSPTLFRVIR1613 LARIGRILRL1623 VKGAKGIRTL 1633 LFALMMSLPA1643 LFNIGLLLFL1653 VMFIYAIFGM1663 SNFAYVKKED1673 GINDMFNFET 1683 FGNSMICLFQ1693 ITTSAGWDGL1703 LAPILNSKPP1713 DCDPKKVHPG1723 SSVEGDCGNP 1733 SVGIFYFVSY1743 IIISFLVVVN1753 MYIAVILENF1763 SVATEESTEP1773 LSEDDFEMFY 1783 EVWEKFDPDA1793 TQFIEFSKLS1803 DFAAALDPPL1813 LIAKPNKVQL1823 IAMDLPMVSG 1833 DRIHCLDILF1843 AFTKRVLGES1853 GEMDSLRSQM1863 EERFMSANPS1873 KVSYEPITTT 1883 LKRKQEDV
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| PDB ID: 6J8I Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 up) | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [2] |
| PDB Sequence |
PLRRISIKIL
123 VHSLFSMLIM133 CTILTNCIFM143 TMNNPPDWTK153 NVEYTFTGIY163 TFESLVKILA 173 RGFCVGEFTF183 LRDPWNWLDF193 VVIVFAYLTE203 FVNLGNVSAL213 RTFRVLRALK 223 TISVIPGLKT233 IVGALIQSVK243 KLSDVMILTV253 FCLSVFALIG263 LQLFMGNLKH 273 KCFRNSLENN283 ETLESIMNTL293 ESEEDFRKYF303 YYLEGSKDAL313 LCGFSTDSGQ 323 CPEGYTCVKI333 GRNPDYGYTS343 FDTFSWAFLA353 LFRLMTQDYW363 ENLYQQTLRA 373 AGKTYMIFFV383 VVIFLGSFYL393 INLILAVVAM403 AYKEQNQANI413 EEAKCSPYWI 731 KFKKCIYFIV741 MDPFVDLAIT751 ICIVLNTLFM761 AMEHHPMTEE771 FKNVLAIGNL 781 VFTGIFAAEM791 VLKLIAMDPY801 EYFQVGWNIF811 DSLIVTLSLV821 ELFLLSVLRS 836 FRLLRVFKLA846 KSWPTLNMLI856 KIIGNSVGAL866 GNLTLVLAII876 VFIFAVVGMQ 886 LFGKSYKECV896 CKINDDCTLP906 RWHMNDFFHS916 FLIVFRVLCG926 EWIETMWDCM 936 EVAGQAMCLI946 VYMMVMVIGN956 LVVLNLFLAL966 LLSSFSGKIW1178 WNIRKTCYKI 1188 VEHSWFESFI1198 VLMILLSSGA1208 LAFEDIYIER1218 KKTIKIILEY1228 ADKIFTYIFI 1238 LEMLLKWIAY1248 GYKTYFTNAW1258 CWLDFLIVDV1268 SLVTLVANTL1278 GYSDLGPIKS 1288 LRTLRALRPL1298 RALSRFEGMR1308 VVVNALIGAI1318 PSIMNVLLVC1328 LIFWLIFSIM 1338 GVNLFAGKFY1348 ECINTTDGSR1358 FPASQVPNRS1368 ECFALMNVSQ1378 NVRWKNLKVN 1388 FDNVGLGYLS1398 LLQVATFKGW1408 TIIMYAAVDS1418 VNVDKQPKYE1428 YSLYMYIYFV 1438 VFIIFGSFFT1448 LNLFIGVIID1458 NFNQQKKKLG1468 GQDIFMTEEQ1478 KKYYNAMKKL 1488 GSKKPQKPIP1498 RPGNKIQGCI1508 FDLVTNQAFD1518 ISIMVLICLN1528 MVTMMVEKEG 1538 QSQHMTEVLY1548 WINVVFIILF1558 TGECVLKLIS1568 LRHYYFTVGW1578 NIFDFVVVII 1588 SIVGMFLADL1598 IETYFVSPTL1608 FRVIRLARIG1618 RILRLVKGAK1628 GIRTLLFALM 1638 MSLPALFNIG1648 LLLFLVMFIY1658 AIFGMSNFAY1668 VKKEDGINDM1678 FNFETFGNSM 1688 ICLFQITTSA1698 GWDGLLAPIL1708 NSKPPDCDPK1718 KVHPGSSVEG1728 DCGNPSVGIF 1738 YFVSYIIISF1748 LVVVNMYIAV1758 ILENFSVATE1768
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| PDB ID: 6J8J Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 down) | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [2] |
| PDB Sequence |
PLRRISIKIL
123 VHSLFSMLIM133 CTILTNCIFM143 TMNNPPDWTK153 NVEYTFTGIY163 TFESLVKILA 173 RGFCVGEFTF183 LRDPWNWLDF193 VVIVFAYLTE203 FVNLGNVSAL213 RTFRVLRALK 223 TISVIPGLKT233 IVGALIQSVK243 KLSDVMILTV253 FCLSVFALIG263 LQLFMGNLKH 273 KCFRNSLENN283 ETLESIMNTL293 ESEEDFRKYF303 YYLEGSKDAL313 LCGFSTDSGQ 323 CPEGYTCVKI333 GRNPDYGYTS343 FDTFSWAFLA353 LFRLMTQDYW363 ENLYQQTLRA 373 AGKTYMIFFV383 VVIFLGSFYL393 INLILAVVAM403 AYKEQNQANI413 EEAKCSPYWI 731 KFKKCIYFIV741 MDPFVDLAIT751 ICIVLNTLFM761 AMEHHPMTEE771 FKNVLAIGNL 781 VFTGIFAAEM791 VLKLIAMDPY801 EYFQVGWNIF811 DSLIVTLSLV821 ELFLLSVLRS 836 FRLLRVFKLA846 KSWPTLNMLI856 KIIGNSVGAL866 GNLTLVLAII876 VFIFAVVGMQ 886 LFGKSYKECV896 CKINDDCTLP906 RWHMNDFFHS916 FLIVFRVLCG926 EWIETMWDCM 936 EVAGQAMCLI946 VYMMVMVIGN956 LVVLNLFLAL966 LLSSFSGKIW1178 WNIRKTCYKI 1188 VEHSWFESFI1198 VLMILLSSGA1208 LAFEDIYIER1218 KKTIKIILEY1228 ADKIFTYIFI 1238 LEMLLKWIAY1248 GYKTYFTNAW1258 CWLDFLIVDV1268 SLVTLVANTL1278 GYSDLGPIKS 1288 LRTLRALRPL1298 RALSRFEGMR1308 VVVNALIGAI1318 PSIMNVLLVC1328 LIFWLIFSIM 1338 GVNLFAGKFY1348 ECINTTDGSR1358 FPASQVPNRS1368 ECFALMNVSQ1378 NVRWKNLKVN 1388 FDNVGLGYLS1398 LLQVATFKGW1408 TIIMYAAVDS1418 VNVDKQPKYE1428 YSLYMYIYFV 1438 VFIIFGSFFT1448 LNLFIGVIID1458 NFNQQKKKLG1468 GQDIFMTEEQ1478 KKYYNAMKKL 1488 GSKKPQKPIP1498 RPGNKIQGCI1508 FDLVTNQAFD1518 ISIMVLICLN1528 MVTMMVEKEG 1538 QSQHMTEVLY1548 WINVVFIILF1558 TGECVLKLIS1568 LRHYYFTVGW1578 NIFDFVVVII 1588 SIVGMFLADL1598 IETYFVSPTL1608 FRVIRLARIG1618 RILRLVKGAK1628 GIRTLLFALM 1638 MSLPALFNIG1648 LLLFLVMFIY1658 AIFGMSNFAY1668 VKKEDGINDM1678 FNFETFGNSM 1688 ICLFQITTSA1698 GWDGLLAPIL1708 NSKPPDCDPK1718 KVHPGSSVEG1728 DCGNPSVGIF 1738 YFVSYIIISF1748 LVVVNMYIAV1758 ILENFSVATE1768
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | High-resolution structures of human Na(v)1.7 reveal gating modulation through Alpha-Pi helical transition of S6(IV). Cell Rep. 2022 Apr 26;39(4):110735. | ||||
| REF 2 | Structures of human Na(v)1.7 channel in complex with auxiliary subunits and animal toxins. Science. 2019 Mar 22;363(6433):1303-1308. | ||||
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