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 | Phosphatidylserine | Ligand Info | |||
| Canonical SMILES | CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCCCCCCCCCCCC | ||||
| InChI | 1S/C42H82NO10P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(44)50-35-38(36-51-54(48,49)52-37-39(43)42(46)47)53-41(45)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h38-39H,3-37,43H2,1-2H3,(H,46,47)(H,48,49)/t38-,39+/m1/s1 | ||||
| InChIKey | TZCPCKNHXULUIY-RGULYWFUSA-N | ||||
| PubChem Compound ID | 9547096 | ||||
| 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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LEU388
3.733
TRP1178
4.061
TRP1179
2.766
ARG1182
3.399
LYS1183
4.254
TYR1186
4.243
LEU1242
4.037
TRP1245
3.234
ILE1246
4.138
ALA1247
3.647
TYR1248
4.217
GLY1249
3.540
TYR1250
3.474
LYS1251
4.577
THR1252
4.382
GLY1489
3.179
GLN1505
4.209
VAL1563
3.916
LEU1566
3.296
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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 .P5S or .P5S2 or .P5S3 or :3P5S;style chemicals stick;color identity;select .A:254 or .A:388 or .A:1178 or .A:1179 or .A:1182 or .A:1183 or .A:1186 or .A:1242 or .A:1245 or .A:1246 or .A:1247 or .A:1248 or .A:1249 or .A:1250 or .A:1251 or .A:1252 or .A:1489 or .A:1490 or .A:1563 or .A:1566 or .A:1567 or .A:1569 or .A:1570 or .A:1571 or .A:1574 or .A:1577 or .A:1578 or .A:1581 or .A:1583 or .A:1621 or .A:1624 or .A:1628 or .A:1631 or .A:1632 or .A:1634 or .A:1635 or .A:1637 or .A:1638 or .A:1641 or .A:1766; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE254
4.631
LEU388
3.915
TRP1178
4.254
TRP1179
2.736
ARG1182
2.926
LYS1183
4.309
TYR1186
3.876
LEU1242
4.265
TRP1245
3.473
ILE1246
3.876
ALA1247
3.859
TYR1248
3.854
GLY1249
3.746
TYR1250
2.818
LYS1251
4.343
THR1252
4.247
GLY1489
3.737
SER1490
3.103
VAL1563
4.789
LEU1566
3.553
ILE1567
4.275
LEU1569
4.833
ARG1570
2.438
HIS1571
3.118
PHE1574
3.964
GLY1577
4.630
TRP1578
2.932
PHE1581
3.823
PHE1583
4.573
LEU1621
4.104
VAL1624
3.431
LYS1628
4.698
ARG1631
3.417
THR1632
3.955
LEU1634
3.587
PHE1635
3.410
LEU1637
4.164
MET1638
4.013
LEU1641
4.285
ALA1766
4.118
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| 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 | [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 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P5S or .P5S2 or .P5S3 or :3P5S;style chemicals stick;color identity;select .A:1178 or .A:1179 or .A:1182 or .A:1183 or .A:1186 or .A:1242 or .A:1245 or .A:1246 or .A:1247 or .A:1248 or .A:1249 or .A:1250 or .A:1251 or .A:1252; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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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 | [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 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P5S or .P5S2 or .P5S3 or :3P5S;style chemicals stick;color identity;select .A:388 or .A:1178 or .A:1179 or .A:1182 or .A:1183 or .A:1186 or .A:1242 or .A:1245 or .A:1246 or .A:1247 or .A:1248 or .A:1249 or .A:1250 or .A:1251 or .A:1252 or .A:1488 or .A:1489 or .A:1490 or .A:1577 or .A:1578 or .A:1581 or .A:1621 or .A:1624 or .A:1628 or .A:1631 or .A:1632 or .A:1634 or .A:1635 or .A:1637 or .A:1638 or .A:1641 or .A:1765 or .A:1769; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU388
3.673
TRP1178
3.956
TRP1179
2.975
ARG1182
2.565
LYS1183
4.284
TYR1186
3.756
LEU1242
3.752
TRP1245
3.588
ILE1246
4.467
ALA1247
3.211
TYR1248
3.722
GLY1249
4.194
TYR1250
3.016
LYS1251
4.178
THR1252
3.820
LEU1488
4.910
GLY1489
4.100
|
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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 | [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 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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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .P5S or .P5S2 or .P5S3 or :3P5S;style chemicals stick;color identity;select .A:254 or .A:388 or .A:1178 or .A:1179 or .A:1182 or .A:1183 or .A:1186 or .A:1242 or .A:1245 or .A:1246 or .A:1247 or .A:1248 or .A:1249 or .A:1250 or .A:1251 or .A:1252 or .A:1488 or .A:1489 or .A:1490 or .A:1492 or .A:1505 or .A:1563 or .A:1566 or .A:1567 or .A:1570 or .A:1571 or .A:1574 or .A:1577 or .A:1578 or .A:1581 or .A:1583 or .A:1621 or .A:1624 or .A:1628 or .A:1631 or .A:1632 or .A:1634 or .A:1635 or .A:1637 or .A:1638 or .A:1641; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
PHE254
4.734
LEU388
3.389
TRP1178
3.455
TRP1179
3.199
ARG1182
2.905
LYS1183
4.517
TYR1186
3.461
LEU1242
3.683
TRP1245
3.700
ILE1246
3.314
ALA1247
3.220
TYR1248
3.586
GLY1249
3.687
TYR1250
3.379
LYS1251
4.012
THR1252
3.603
LEU1488
4.722
GLY1489
3.911
SER1490
3.946
LYS1492
2.879
GLN1505
4.513
VAL1563
4.912
LEU1566
4.615
ILE1567
3.818
ARG1570
4.583
HIS1571
2.856
PHE1574
4.176
GLY1577
4.380
TRP1578
2.647
PHE1581
3.688
PHE1583
4.983
LEU1621
4.232
VAL1624
3.409
LYS1628
4.980
ARG1631
3.000
THR1632
4.580
LEU1634
2.747
PHE1635
3.858
LEU1637
3.784
MET1638
3.253
LEU1641
4.204
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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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