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 | N-acetylsphingosine 1-phosphate | Ligand Info | |||
| Canonical SMILES | CCCCCCCCCCCCCC=CC(C(COP(=O)(O)O)NC(=O)C)O | ||||
| InChI | 1S/C20H40NO6P/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-20(23)19(21-18(2)22)17-27-28(24,25)26/h15-16,19-20,23H,3-14,17H2,1-2H3,(H,21,22)(H2,24,25,26)/b16-15+/t19-,20+/m0/s1 | ||||
| InChIKey | HWPZKJVGDYNEAW-QUDYQQOWSA-N | ||||
| PubChem Compound ID | 15199918 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7XVE Human Nav1.7 mutant class-I | ||||||
| Method | Electron microscopy | Resolution | 2.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
GPQSFVHFTK
17 QSLALIEQRI27 AERKSKEPKP49 SSDLEAGKQL59 PFIYGDIPPG69 MVSEPLEDLD 79 PYYADKKTFI89 VLNKGKTIFR99 FNATPALYML109 SPFSPLRRIS119 IKILVHSLFS 129 MLIMCTILTN139 CIFMTMNNPP149 DWTKNVKYTF159 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 VVAMAYEEQN409 QANIEEAKQK419 ELEFQQMLCS 727 PYWIKFKKCI737 YFIVMDPFVD747 LAITICIVLN757 TLFMAMEHHP767 MTEEFKNVLA 777 IRNLVFTGIF787 AAEMVLKLIA797 MDPYEYFQVG807 WNIFDSLIVT817 LSLVELFGLS 832 VLRSFRLLRV842 FKLAKSWPTL852 NMLIKIIGNS862 VGAFGNLMLV872 LFIIVFIFAV 882 VGMQLFGKSY892 KECVCKINDD902 CTLPRWHMND912 FFHSFLIVFR922 VLCGEWIETM 932 WDCMEVAGQA942 MCLIFYMMVF952 FIGNLVVLNL962 FLALLLSSFS972 SDANNLQIAV 992 TRIKKGINYV1002 KQTLREFILK1012 AFGKIWWNIR1182 KTCYKIVEHS1192 WFESFIVLMI 1202 LLSSGALAFE1212 DIYIERKKTI1222 KIILEYADKI1232 FTYIFILEML1242 LKWIAYGYKT 1252 YFTNAWCWLD1262 FLIVDVSLVT1272 LVANTLGYSD1282 LGPIKSLRTL1292 RALRPLRALS 1302 RFEGMRVVVN1312 ALIGAIPSIM1322 NVLLVCLIFW1332 LIFSIMGVNL1342 FAGKFYECIN 1352 TTDGSRFPAS1362 QVPNRSECFA1372 LMNVSQNVRW1382 KNLKVNFDNV1392 GLGYLSLLQV 1402 ATFKGWTIIM1412 YAAVDSVNVD1422 KQPKYEYSLY1432 MYIYFIFFII1442 FGSFFTLNLF 1452 ICVIIDNFNQ1462 QKKKLGGQDI1472 FMTEEQKKYY1482 NAMKKLGSKK1492 PQKPIPRPGN 1502 KIQGCIFDLV1512 TNQAFDISIM1522 VLICLNMVTM1532 MVEKEGQSQH1542 MTEVLYWINV 1552 VFIILFTGEC1562 VLKLISLRHY1572 YFTVGWNIFD1582 FVVVIISIVG1592 MFLADLIETY 1602 FVSPTLFRVI1612 RLARIGRILR1622 LVKGAKGIRT1632 LLFALMMSLP1642 ALFNIGLLLF 1652 LVMFIYAIFG1662 MSNFAYVKKE1672 DGINDMFNFE1682 TFGNSMICLF1692 QITTSAGWDG 1702 LLAPILNSKP1712 PDCDPKKVHP1722 GSSVEGDCGN1732 PSVGIFYFVS1742 YIIISFLVVV 1752 NMYIAVILEN1762 FSVATE
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| PDB ID: 7XVF Nav1.7 mutant class2 | ||||||
| Method | Electron microscopy | Resolution | 2.80 Å | Mutation | Yes | [1] |
| PDB Sequence |
GPQSFVHFTK
17 QSLALIEQRI27 AERKSKEPKP49 SSDLEAGKQL59 PFIYGDIPPG69 MVSEPLEDLD 79 PYYADKKTFI89 VLNKGKTIFR99 FNATPALYML109 SPFSPLRRIS119 IKILVHSLFS 129 MLIMCTILTN139 CIFMTMNNPP149 DWTKNVKYTF159 TGIYTFESLV169 KILARGFCVG 179 EFTFLRDPWN189 WLDFVVIVFA199 YLTEFVNVSA212 LRTFRVLRAL222 KTISVIPGLK 232 TIVGALIQSV242 KKLSDVMILT252 VFCLSVFALI262 GLQLFMGNLK272 HKCFRNSLEN 282 NETLESIMNT292 LESEEDFRKY302 FYYLEGSKDA312 LLCGFSTDSG322 QCPEGYTCVK 332 IGRNPDYGYT342 SFDTFSWAFL352 ALFRLMTQDY362 WENLYQQTLR372 AAGKTYMIFF 382 VVVIFLGSFY392 LINLILAVVA402 MAYEEQNQAN412 IEEAKCSPYW730 IKFKKCIYFI 740 VMDPFVDLAI750 TICIVLNTLF760 MAMEHHPMTE770 EFKNVLAIRN780 LVFTGIFAAE 790 MVLKLIAMDP800 YEYFQVGWNI810 FDSLIVTLSL820 VELFGLSVLR835 SFRLLRVFKL 845 AKSWPTLNML855 IKIIGNSVGA865 FGNLMLVLFI875 IVFIFAVVGM885 QLFGKSYKEC 895 VCKINDDCTL905 PRWHMNDFFH915 SFLIVFRVLC925 GEWIETMWDC935 MEVAGQAMCL 945 IFYMMVFFIG955 NLVVLNLFLA965 LLLSSFSANN987 LQIAVTRIKK997 GINYVKQTLR 1007 EFILKAFGKI1177 WWNIRKTCYK1187 IVEHSWFESF1197 IVLMILLSSG1207 ALAFEDIYIE 1217 RKKTIKIILE1227 YADKIFTYIF1237 ILEMLLKWIA1247 YGYKTYFTNA1257 WCWLDFLIVD 1267 VSLVTLVANT1277 LGYSDLGPIK1287 SLRTLRALRP1297 LRALSRFEGM1307 RVVVNALIGA 1317 IPSIMNVLLV1327 CLIFWLIFSI1337 MGVNLFAGKF1347 YECINTTDGS1357 RFPASQVPNR 1367 SECFALMNVS1377 QNVRWKNLKV1387 NFDNVGLGYL1397 SLLQVATFKG1407 WTIIMYAAVD 1417 SVNVDKQPKY1427 EYSLYMYIYF1437 IFFIIFGSFF1447 TLNLFICVII1457 DNFNQQKKKL 1467 GGQDIFMTEE1477 QKKYYNAMKK1487 LGSKKPQKPI1497 PRPGNKIQGC1507 IFDLVTNQAF 1517 DISIMVLICL1527 NMVTMMVEKE1537 GQSQHMTEVL1547 YWINVVFIIL1557 FTGECVLKLI 1567 SLRHYYFTVG1577 WNIFDFVVVI1587 ISIVGMFLAD1597 LIETYFVSPT1607 LFRVIRLARI 1617 GRILRLVKGA1627 KGIRTLLFAL1637 MMSLPALFNI1647 GLLLFLVMFI1657 YAIFGMSNFA 1667 YVKKEDGIND1677 MFNFETFGNS1687 MICLFQITTS1697 AGWDGLLAPI1707 LNSKPPDCDP 1717 KKVHPGSSVE1727 GDCGNPSVGI1737 FYFVSYIIIS1747 FLVVVNMYIA1757 VILENFSVAT 1767 E
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| 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 | [2] |
| 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: 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 | [2] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1PW or .1PW2 or .1PW3 or :31PW;style chemicals stick;color identity;select .A:360 or .A:391 or .A:1321 or .A:1325 or .A:1400 or .A:1404 or .A:1452 or .A:1695 or .A:1696 or .A:1697 or .A:1744 or .A:1745 or .A:1747 or .A:1748 or .A:1749 or .A:1752; 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 | Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na(v)1.7. Proc Natl Acad Sci U S A. 2022 Aug 16;119(33):e2209164119. | ||||
| REF 2 | 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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