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 | (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en | Ligand Info | |||
| Canonical SMILES | CC1CCC2(C(C3C(O2)CC4C3(CCC5C4CC=C6C5(CCC(C6)OCCC(COC)COC)C)C)C)OC1 | ||||
| InChI | 1S/C34H56O5/c1-22-9-15-34(38-19-22)23(2)31-30(39-34)18-29-27-8-7-25-17-26(37-16-12-24(20-35-5)21-36-6)10-13-32(25,3)28(27)11-14-33(29,31)4/h7,22-24,26-31H,8-21H2,1-6H3/t22-,23+,26+,27-,28+,29+,30+,31+,32+,33+,34-/m1/s1 | ||||
| InChIKey | CEEBZAXXSRFQIC-GZSGZGDASA-N | ||||
| PubChem Compound ID | 134817783 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7W9K Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution | ||||||
| Method | Electron microscopy | Resolution | 2.20 Å | Mutation | No | [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 AMAYEEQNQA411 NIEEAKQKEL421 EFQQMLDRLK 431 KEQEPYWIKF733 KKCIYFIVMD743 PFVDLAITIC753 IVLNTLFMAM763 EHHPMTEEFK 773 NVLAIGNLVF783 TGIFAAEMVL793 KLIAMDPYEY803 FQVGWNIFDS813 LIVTLSLVEL 823 FLLSVLRSFR838 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: 7W9L Cryo-EM structure of human Nav1.7(E406K)-beta1-beta2 complex | ||||||
| Method | Electron microscopy | Resolution | 3.50 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 LKKEQEPYWI731 KFKKCIYFIV741 MDPFVDLAIT751 ICIVLNTLFM761 AMEHHPMTEE 771 FKNVLAIGNL781 VFTGIFAAEM791 VLKLIAMDPY801 EYFQVGWNIF811 DSLIVTLSLV 821 ELFLADVEGL831 SVLRSFRLLR841 VFKLAKSWPT851 LNMLIKIIGN861 SVGALGNLTL 871 VLAIIVFIFA881 VVGMQLFGKS891 YKECVCKIND901 DCTLPRWHMN911 DFFHSFLIVF 921 RVLCGEWIET931 MWDCMEVAGQ941 AMCLIVYMMV951 MVIGNLVVLN961 LFLALLLSSF 971 SSDNLTAIEE981 DPDANNLQIA991 VTRIKKGINY1001 VKQTLREFIL1011 KAFGKIWWNI 1181 RKTCYKIVEH1191 SWFESFIVLM1201 ILLSSGALAF1211 EDIYIERKKT1221 IKIILEYADK 1231 IFTYIFILEM1241 LLKWIAYGYK1251 TYFTNAWCWL1261 DFLIVDVSLV1271 TLVANTLGYS 1281 DLGPIKSLRT1291 LRALRPLRAL1301 SRFEGMRVVV1311 NALIGAIPSI1321 MNVLLVCLIF 1331 WLIFSIMGVN1341 LFAGKFYECI1351 NTTDGSRFPA1361 SQVPNRSECF1371 ALMNVSQNVR 1381 WKNLKVNFDN1391 VGLGYLSLLQ1401 VATFKGWTII1411 MYAAVDSVNV1421 DKQPKYEYSL 1431 YMYIYFVVFI1441 IFGSFFTLNL1451 FIGVIIDNFN1461 QQKKKLGGQD1471 IFMTEEQKKY 1481 YNAMKKLGSK1491 KPQKPIPRPG1501 NKIQGCIFDL1511 VTNQAFDISI1521 MVLICLNMVT 1531 MMVEKEGQSQ1541 HMTEVLYWIN1551 VVFIILFTGE1561 CVLKLISLRH1571 YYFTVGWNIF 1581 DFVVVIISIV1591 GMFLADLIET1601 YFVSPTLFRV1611 IRLARIGRIL1621 RLVKGAKGIR 1631 TLLFALMMSL1641 PALFNIGLLL1651 FLVMFIYAIF1661 GMSNFAYVKK1671 EDGINDMFNF 1681 ETFGNSMICL1691 FQITTSAGWD1701 GLLAPILNSK1711 PPDCDPKKVH1721 PGSSVEGDCG 1731 NPSVGIFYFV1741 SYIIISFLVV1751 VNMYIAVILE1761 NFSVATEEST1771 EPLSEDDFEM 1781 FYEVWEKFDP1791 DATQFIEFSK1801 LSDFAAALDP1811 PLLIAKPNKV1821 QLIAMDLPMV 1831 SGDRIHCLDI1841 LFAFTKRVLG1851 ESGEMDSLRS1861 QMEERFMSAN1871 PSKVSYEPIT 1881 TTLKRKQEDV1891
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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. | ||||
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