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 | [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate | Ligand Info | |||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7W9P Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV pi helix conformer) | ||||||
| Method | Electron microscopy | Resolution | 2.90 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 YLTEFVNLGN209 VSALRTFRVL219 RALKTISVIP 229 GLKTIVGALI239 QSVKKLSDVM249 ILTVFCLSVF259 ALIGLQLFMG269 NLKHKCFRNS 279 LENNETLESI289 MNTLESEEDF299 RKYFYYLEGS309 KDALLCGFST319 DSGQCPEGYT 329 CVKIGRNPDY339 GYTSFDTFSW349 AFLALFRLMT359 QDYWENLYQQ369 TLRAAGKTYM 379 IFFVVVIFLG389 SFYLINLILA399 VVAMAYKEQN409 QANIEEAKQK419 ELEFQQMLDP 728 YWIKFKKCIY738 FIVMDPFVDL748 AITICIVLNT758 LFMAMEHHPM768 TEEFKNVLAI 778 GNLVFTGIFA788 AEMVLKLIAM798 DPYEYFQVGW808 NIFDSLIVTL818 SLVELFLADV 828 EGLSVLRSFR838 LLRVFKLAKS848 WPTLNMLIKI858 IGNSVGALGN868 LTLVLAIIVF 878 IFAVVGMQLF888 GKSYKECVCK898 INDDCTLPRW908 HMNDFFHSFL918 IVFRVLCGEW 928 IETMWDCMEV938 AGQAMCLIVY948 MMVMVIGNLV958 VLNLFLALLL968 SSFSSDNLTA 978 IEEDPDANNL988 QIAVTRIKKG998 INYVKQTLRE1008 FILKAFGKIW1178 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 ESTEPLSEDD1778 FEMFYEVWEK 1788 FDPDATQFIE1798 FSKLSDFAAA1808 LDPPLLIAKP1818 NKVQLIAMDL1828 PMVSGDRIHC 1838 LDILFAFTKR1848 VLGESGEMDS1858 LRSQMEERFM1868 SANPSKVSYE1878 PITTTLKRKQ 1888 EDV
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| PDB ID: 7W9T Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV alpha 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 YLTEFVNLGN209 VSALRTFRVL219 RALKTISVIP 229 GLKTIVGALI239 QSVKKLSDVM249 ILTVFCLSVF259 ALIGLQLFMG269 NLKHKCFRNS 279 LENNETLESI289 MNTLESEEDF299 RKYFYYLEGS309 KDALLCGFST319 DSGQCPEGYT 329 CVKIGRNPDY339 GYTSFDTFSW349 AFLALFRLMT359 QDYWENLYQQ369 TLRAAGKTYM 379 IFFVVVIFLG389 SFYLINLILA399 VVAMAYKEQN409 QANIEEAKQK419 ELEFQQMLDR 429 LKKPYWIKFK734 KCIYFIVMDP744 FVDLAITICI754 VLNTLFMAME764 HHPMTEEFKN 774 VLAIGNLVFT784 GIFAAEMVLK794 LIAMDPYEYF804 QVGWNIFDSL814 IVTLSLVELF 824 LADVEGLSVL834 RSFRLLRVFK844 LAKSWPTLNM854 LIKIIGNSVG864 ALGNLTLVLA 874 IIVFIFAVVG884 MQLFGKSYKE894 CVCKINDDCT904 LPRWHMNDFF914 HSFLIVFRVL 924 CGEWIETMWD934 CMEVAGQAMC944 LIVYMMVMVI954 GNLVVLNLFL964 ALLLSSFSSD 974 NLTAIEEDPD984 ANNLQIAVTR994 IKKGINYVKQ1004 TLREFILKAF1014 GKIWWNIRKT 1184 CYKIVEHSWF1194 ESFIVLMILL1204 SSGALAFEDI1214 YIERKKTIKI1224 ILEYADKIFT 1234 YIFILEMLLK1244 WIAYGYKTYF1254 TNAWCWLDFL1264 IVDVSLVTLV1274 ANTLGYSDLG 1284 PIKSLRTLRA1294 LRPLRALSRF1304 EGMRVVVNAL1314 IGAIPSIMNV1324 LLVCLIFWLI 1334 FSIMGVNLFA1344 GKFYECINTT1354 DGSRFPASQV1364 PNRSECFALM1374 NVSQNVRWKN 1384 LKVNFDNVGL1394 GYLSLLQVAT1404 FKGWTIIMYA1414 AVDSVNVDKQ1424 PKYEYSLYMY 1434 IYFVVFIIFG1444 SFFTLNLFIG1454 VIIDNFNQQK1464 KKLGGQDIFM1474 TEEQKKYYNA 1484 MKKLGSKKPQ1494 KPIPRPGNKI1504 QGCIFDLVTN1514 QAFDISIMVL1524 ICLNMVTMMV 1534 EKEGQSQHMT1544 EVLYWINVVF1554 IILFTGECVL1564 KLISLRHYYF1574 TVGWNIFDFV 1584 VVIISIVGMF1594 LADLIETYFV1604 SPTLFRVIRL1614 ARIGRILRLV1624 KGAKGIRTLL 1634 FALMMSLPAL1644 FNIGLLLFLV1654 MFIYAIFGMS1664 NFAYVKKEDG1674 INDMFNFETF 1684 GNSMICLFQI1694 TTSAGWDGLL1704 APILNSKPPD1714 CDPKKVHPGS1724 SVEGDCGNPS 1734 VGIFYFVSYI1744 IISFLVVVNM1754 YIAVILENFS1764 VATEESTEPL1774 SEDDFEMFYE 1784 VWEKFDPDAT1794 QFIEFSKLSD1804 FAAALDPPLL1814 IAKPNKVQLI1824 AMDLPMVSGD 1834 RIHCLDILFA1844 FTKRVLGESG1854 EMDSLRSQME1864 ERFMSANPSK1874 VSYEPITTTL 1884 KRKQEDV
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| PDB ID: 6J8G Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (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: 6J8H Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9SL or .9SL2 or .9SL3 or :39SL;style chemicals stick;color identity;select .A:362 or .A:363 or .A:364 or .A:922 or .A:927 or .A:930 or .A:1405 or .A:1406 or .A:1407 or .A:1408 or .A:1409 or .A:1410 or .A:1698 or .A:1699 or .A:1700 or .A:1701 or .A:1702; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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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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