Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T43739 | Target Info | |||
| Target Name | Voltage-gated sodium channel alpha Nav1.8 (SCN10A) | ||||
| Synonyms | hPN3; Voltage-gated sodium channel subunit alpha Nav1.8; Sodium channel protein type X subunit alpha; Sodium channel protein type 10 subunit alpha; Peripheral nerve sodium channel 3; PN3 | ||||
| Target Type | Successful Target | ||||
| Gene Name | SCN10A | ||||
| 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: 7WE4 Human Nav1.8 with A-803467, class I | ||||||
| Method | Electron microscopy | Resolution | 2.70 Å | Mutation | No | [1] |
| PDB Sequence |
LIRRTAIKVS
127 VHSWFSLFIT137 VTILVNCVCM147 TRTDLPEKIE157 YVFTVIYTFE167 ALIKILARGF 177 CLNEFTYLRD187 PWNWLDFSVI197 TLAYVGTAID207 LRGISGLRTF217 RVLRALKTVS 227 VIPGLKVIVG237 ALIHSVKKLA247 DVTILTIFCL257 SVFALVGLQL267 FKGNLKNKCV 277 KNDMAYSSHR293 KPDIYINKRG303 TSDPLLCGNG313 SDSGHCPDGY323 ICLKTSDNPD 333 FNYTSFDSFA343 WAFLSLFRLM353 TQDSWERLYQ363 QTLRTSGKIY373 MIFFVLVIFL 383 GSFYLVNLIL393 AVVTMAYEEQ403 NQATWVKLKT656 ILFGLVTDPF666 AELTITLCIV 676 VNTIFMAMEH686 HGMSPTFEAM696 LQIGNIVFTI706 FFTAEMVFKI716 IAFDPYYYFQ 726 KKWNIFDCII736 VTVSLLELGV746 AKKGSLSVLR756 SFRLLRVFKL766 AKSWPTLNTL 776 IKIIGNSVGA786 LGNLTIILAI796 IVFVFALVGK806 QLLGENYRNN816 RKNISAPHED 826 WPRWHMHDFF836 HSFLIVFRIL846 CGEWIENMWA856 CMEVGQKSIC866 LILFLTVMVL 876 GNLVVLNLFI886 ALLLNSFFAD1136 VGWQVRKTCY1146 RIVEHSWFES1156 FIIFMILLSS 1166 GSLAFEDYYL1176 DQKPTVKALL1186 EYTDRVFTFI1196 FVFEMLLKWV1206 AYGFKKYFTN 1216 AWCWLDFLIV1226 NISLISLTAK1236 ILEYSEVAPI1246 KALRTLRALR1256 PLRALSRFEG 1266 MRVVVDALVG1276 AIPSIMNVLL1286 VCLIFWLIFS1296 IMGVNLFAGK1306 FWRCINYTDG 1316 EFSLVPLSIV1326 NNKSDCKIQN1336 STGSFFWVNV1346 KVNFDNVAMG1356 YLALLQVATF 1366 KGWMDIMYAA1376 VDSREVNMQP1386 KWEDNVYMYL1396 YFVIFIIFGG1406 FFTLNLFVGV 1416 IIDNFNQQKK1426 KLGGQDIFMT1436 EEQKKYYNAM1446 KKLGSKKPQK1456 PIPRPLNKFQ 1466 GFVFDIVTRQ1476 AFDITIMVLI1486 CLNMITMMVE1496 TDDQSEEKTK1506 ILGKINQFFV 1516 AVFTGECVMK1526 MFALRQYYFT1536 NGWNVFDFIV1546 VVLSIASLIF1556 SAILKSLQSY 1566 FSPTLFRVIR1576 LARIGRILRL1586 IRAAKGIRTL1596 LFALMMSLPA1606 LFNIGLLLFL 1616 VMFIYSIFGM1626 SSFPHVRWEA1636 GIDDMFNFQT1646 FANSMLCLFQ1656 ITTSAGWDGL 1666 LSPILNTGPP1676 YCDPNLPNSN1686 GTRGDCGSPA1696 VGIIFFTTYI1706 IISFLIMVNM 1716 YIAVILENFN1726 VA
|
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|
|
ILE254
4.866
LEU257
4.720
TYR336
3.523
ALA343
4.053
TRP344
3.333
PHE346
4.075
LEU347
4.024
PHE350
3.350
MET858
4.696
LYS863
3.309
SER864
3.744
LEU867
3.970
ILE868
4.149
LEU871
2.793
THR872
3.553
VAL875
4.532
LEU1285
3.863
CYS1288
3.658
LEU1289
3.949
TRP1292
3.883
ASN1352
3.826
ALA1354
3.456
MET1355
3.654
TYR1357
4.386
LEU1358
4.189
LEU1361
3.938
PHE1468
3.533
ASP1471
4.793
ILE1472
3.590
ARG1475
2.678
ALA1477
4.218
PHE1478
3.881
THR1481
4.403
ILE1482
4.562
VAL1518
4.034
MET1525
3.483
THR1673
4.642
PRO1695
3.707
ALA1696
3.592
ILE1699
3.685
ILE1700
3.885
THR1703
3.815
THR1704
3.751
ILE1707
3.584
|
|||||
| PDB ID: 7WFR Human Nav1.8 with A-803467, class III | ||||||
| Method | Electron microscopy | Resolution | 3.00 Å | Mutation | No | [1] |
| PDB Sequence |
SWFSLFITVT
139 ILVNCVCMTR149 TDLPEKIEYV159 FTVIYTFEAL169 IKILARGDPW189 NWLDFSVITL 199 AYVGTAIDLR209 GISGLRTFRV219 LRALKTVSVI229 PGLKVIVGAL239 IHSVKKLADV 249 TILTIFCLSV259 FALVGLQLFK269 GNLKNKCVKN279 DMAYSSHRKP295 DIYINKRGTS 305 DPLLCGNGSD315 SGHCPDGYIC325 LKTSDNPDFN335 YTSFDSFAWA345 FLSLFRLMTQ 355 DSWERLYQQT365 LRTSGKIYMI375 FFVLVIFLGS385 FYLVNLILAV395 VTMAYEEQNQ 405 ATWVKLKTIL658 FGLVTDPFAE668 LTITLCIVVN678 TIFMAMEHHG688 MSPTFEAMLQ 698 IGNIVFTIFF708 TAEMVFKIIA718 FDPYYYFQKK728 WNIFDCIIVT738 VSLLELGVAK 748 KGSLSVLRSF758 RLLRVFKLAK768 SWPTLNTLIK778 IIGNSVGALG788 NLTIILAIIV 798 FVFALVGKQL808 LGENYRNNRK818 NISAPHEDWP828 RWHMHDFFHS838 FLIVFRILCG 848 EWIENMWACM858 EVGQKSICLI868 LFLTVMVLGN878 LVVLNLFIAL888 LLNSFFADVG 1138 WQVRKTCYRI1148 VEHSWFESFI1158 IFMILLSSGS1168 LAFEDYYLDQ1178 KPTVKALLEY 1188 TDRVFTFIFV1198 FEMLLKWVAY1208 GFKKYFTNAW1218 CWLDFLIVNI1228 SLISLTAKIL 1238 EYSEVAPIKA1248 LRTLRALRPL1258 RALSRFEGMR1268 VVVDALVGAI1278 PSIMNVLLVC 1288 LIFWLIFSIM1298 GVNLFAGKFW1308 RCINYTDGEF1318 SLVPLSIVNN1328 KSDCKIQNST 1338 GSFFWVNVKV1348 NFDNVAMGYL1358 ALLQVATFKG1368 WMDIMYAAVD1378 SREVNMQPKW 1388 EDNVYMYLYF1398 VIFIIFGGFF1408 TLNLFVGVII1418 DNFNQQKKKL1428 GGQDIFMTEE 1438 QKKYYNAMKK1448 LGSKKPQKPI1458 PRPLNKFQGF1468 VFDIVTRQAF1478 DITIMVLICL 1488 NMITMMVETD1498 DQSEEKTKIL1508 GKINQFFVAV1518 FTGECVMKMF1528 ALRQYYFTNG 1538 WNVFDFIVVV1548 LSIASLIFSA1558 ILKSLQSYFS1568 PTLFRVIRLA1578 RIGRILRLIR 1588 AAKGIRTLLF1598 ALMMSLPALF1608 NIGLLLFLVM1618 FIYSIFGMSS1628 FPHVRWEAGI 1638 DDMFNFQTFA1648 NSMLCLFQIT1658 TSAGWDGLLS1668 PILNTGPPYC1678 DPNLPNSNGT 1688 RGDCGSPAVG1698 IIFFTTYIII1708 SFLIMVNMYI1718 AVILENFNVA1728 |
|||||
|
|
LEU1285
4.478
CYS1288
3.350
LEU1289
3.897
TRP1292
3.744
ASN1349
4.856
ASP1351
4.890
ASN1352
3.144
ALA1354
3.588
MET1355
3.965
TYR1357
4.210
|
|||||
| PDB ID: 7WFW Apo human Nav1.8 | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | No | [1] |
| PDB Sequence |
LKVIVGALIH
241 SVKKLADVTI251 LTIFCLSVFA261 LVGLQLFKGN271 LKNKCVKNDP295 DIYINKRGTS 305 DPLLCGNGSD315 SGHCPDGYIC325 LKTSDNPDFN335 YTSFDSFAWA345 FLSLFRLMTQ 355 DSWERLYQQT365 LRTSGKIYMI375 FFVLVIFLGS385 FYLVNLILAV395 VTMAYEEQNQ 405 ATWVKLKTIL658 FGLVTDPFAE668 LTITLCIVVN678 TIFMAMEHHG688 MSPTFEAMLQ 698 IGNIVFTIFF708 TAEMVFKIIA718 FDPYYYFQKK728 WNIFDCIIVT738 VSLLELGVAK 748 KGSLSVLRSF758 RLLRVFKLAK768 SWPTLNTLIK778 IIGNSVGALG788 NLTIILAIIV 798 FVFALVGKQL808 LGENYRNNRK818 NISAPHEDWP828 RWHMHDFFHS838 FLIVFRILCG 848 EWIENMWACM858 EVGQKSICLI868 LFLTVMVLGN878 LVVLNLFIAL888 LLNSFFADVG 1138 WQVRKTCYRI1148 VEHSWFESFI1158 IFMILLSSGS1168 LAFEDYYLDQ1178 KPTVKALLEY 1188 TDRVFTFIFV1198 FEMLLKWVAY1208 GFKKYFTNAW1218 CWLDFLIVNI1228 SLISLTAKIL 1238 EYSEVAPIKA1248 LRTLRALRPL1258 RALSRFEGMR1268 VVVDALVGAI1278 PSIMNVLLVC 1288 LIFWLIFSIM1298 GVNLFAGKFW1308 RCINYTDGEF1318 SLVPLSIVNN1328 KSDCKIQNST 1338 GSFFWVNVKV1348 NFDNVAMGYL1358 ALLQVATFKG1368 WMDIMYAAVD1378 SREVNMQPKW 1388 EDNVYMYLYF1398 VIFIIFGGFF1408 TLNLFVGVII1418 DNFNQQKKKL1428 GGQDIFMTEE 1438 QKKYYNAMKK1448 LGSKKPQKPI1458 PRPLNKFQGF1468 VFDIVTRQAF1478 DITIMVLICL 1488 NMITMMVETD1498 DQSEEKTKIL1508 GKINQFFVAV1518 FTGECVMKMF1528 ALRQYYFTNG 1538 WNVFDFIVVV1548 LSIASLIFSA1558 ILKSLQSYFS1568 PTLFRVIRLA1578 RIGRILRLIR 1588 AAKGIRTLLF1598 ALMMSLPALF1608 NIGLLLFLVM1618 FIYSIFGMSS1628 FPHVRWEAGI 1638 DDMFNFQTFA1648 NSMLCLFQIT1658 TSAGWDGLLS1668 PILNTGPPYC1678 DPNLPNSNGT 1688 RGDCGSPAVG1698 IIFFTTYIII1708 SFLIMVNMYI1718 AVILENFN
|
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|
|
ILE254
4.823
LEU257
4.599
TYR336
4.129
ALA343
4.160
TRP344
2.979
PHE346
4.013
LEU347
4.139
PHE350
3.656
MET858
4.891
LYS863
3.226
SER864
3.601
LEU867
3.230
ILE868
4.285
LEU871
3.100
THR872
3.551
VAL875
4.365
LEU876
4.957
|
|||||
| PDB ID: 7WEL Human Nav1.8 with A-803467, class II | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | No | [1] |
| PDB Sequence |
HSWFSLFITV
138 TILVNCVCMT148 RTDLPEKIEY158 VFTVIYTFEA168 LIKILARGFD187 PWNWLDFSVI 197 TLAYVGTAID207 LRGISGLRTF217 RVLRALKTVS227 VIPGLKVIVG237 ALIHSVKKLA 247 DVTILTIFCL257 SVFALVGLQL267 FKGNLKNKCV277 KNDMAYSSHR293 KPDIYINKRG 303 TSDPLLCGNG313 SDSGHCPDGY323 ICLKTSDNPD333 FNYTSFDSFA343 WAFLSLFRLM 353 TQDSWERLYQ363 QTLRTSGKIY373 MIFFVLVIFL383 GSFYLVNLIL393 AVVTMAYEEQ 403 NQATWVKLKT656 ILFGLVTDPF666 AELTITLCIV676 VNTIFMAMEH686 HGMSPTFEAM 696 LQIGNIVFTI706 FFTAEMVFKI716 IAFDPYYYFQ726 KKWNIFDCII736 VTVSLLELGV 746 AKKGSLSVLR756 SFRLLRVFKL766 AKSWPTLNTL776 IKIIGNSVGA786 LGNLTIILAI 796 IVFVFALVGK806 QLLGENYRNN816 RKNISAPHED826 WPRWHMHDFF836 HSFLIVFRIL 846 CGEWIENMWA856 CMEVGQKSIC866 LILFLTVMVL876 GNLVVLNLFI886 ALLLNSFFAD 1136 VGWQVRKTCY1146 RIVEHSWFES1156 FIIFMILLSS1166 GSLAFEDYYL1176 DQKPTVKALL 1186 EYTDRVFTFI1196 FVFEMLLKWV1206 AYGFKKYFTN1216 AWCWLDFLIV1226 NISLISLTAK 1236 ILEYSEVAPI1246 KALRTLRALR1256 PLRALSRFEG1266 MRVVVDALVG1276 AIPSIMNVLL 1286 VCLIFWLIFS1296 IMGVNLFAGK1306 FWRCINYTDG1316 EFSLVPLSIV1326 NNKSDCKIQN 1336 STGSFFWVNV1346 KVNFDNVAMG1356 YLALLQVATF1366 KGWMDIMYAA1376 VDSREVNMQP 1386 KWEDNVYMYL1396 YFVIFIIFGG1406 FFTLNLFVGV1416 IIDNFNQQKK1426 KLGGQDIFMT 1436 EEQKKYYNAM1446 KKLGSKKPQK1456 PIPRPLNKFQ1466 GFVFDIVTRQ1476 AFDITIMVLI 1486 CLNMITMMVE1496 TDDQSEEKTK1506 ILGKINQFFV1516 AVFTGECVMK1526 MFALRQYYFT 1536 NGWNVFDFIV1546 VVLSIASLIF1556 SAILKSLQSY1566 FSPTLFRVIR1576 LARIGRILRL 1586 IRAAKGIRTL1596 LFALMMSLPA1606 LFNIGLLLFL1616 VMFIYSIFGM1626 SSFPHVRWEA 1636 GIDDMFNFQT1646 FANSMLCLFQ1656 ITTSAGWDGL1666 LSPILNTGPP1676 YCDPNLPNSN 1686 GTRGDCGSPA1696 VGIIFFTTYI1706 IISFLIMVNM1716 YIAVILENFN1726 VA |
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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:257 or .A:336 or .A:343 or .A:344 or .A:346 or .A:347 or .A:350 or .A:858 or .A:863 or .A:864 or .A:867 or .A:868 or .A:871 or .A:872 or .A:875 or .A:1285 or .A:1288 or .A:1289 or .A:1292 or .A:1352 or .A:1354 or .A:1355 or .A:1357 or .A:1358 or .A:1361 or .A:1673 or .A:1695 or .A:1696 or .A:1699 or .A:1700 or .A:1703 or .A:1704 or .A:1707; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE254
4.214
LEU257
4.520
TYR336
3.490
ALA343
4.069
TRP344
3.338
PHE346
4.052
LEU347
4.018
PHE350
3.299
MET858
4.952
LYS863
2.727
SER864
3.671
LEU867
3.907
ILE868
4.551
LEU871
3.140
THR872
3.540
VAL875
4.405
LEU1285
4.094
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for high-voltage activation and subtype-specific inhibition of human Na(v)1.8. Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2208211119. | ||||
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