Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T76937 | Target Info | |||
| Target Name | Voltage-gated sodium channel alpha Nav1.3 (SCN3A) | ||||
| Synonyms | Voltage-gated sodium channel subunit alpha Nav1.3; Voltage-gated sodium channel subtype III; Sodium channel protein, brain III subunit alpha; Sodium channel protein type III subunit alpha; Sodium channel protein type 3 subunit alpha; Sodium channel protein brain III subunit alpha; NAC3; KIAA1356 | ||||
| Target Type | Successful Target | ||||
| Gene Name | SCN3A | ||||
| Biochemical Class | Voltage-gated ion channel | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine | Ligand Info | |||
| Canonical SMILES | CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)([O-])OCC[NH3+])OC(=O)CCCCCCCC=CCCCCCCCC | ||||
| InChI | 1S/C39H76NO8P/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-39(42)48-37(36-47-49(43,44)46-34-33-40)35-45-38(41)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h17-18,37H,3-16,19-36,40H2,1-2H3,(H,43,44)/b18-17-/t37-/m1/s1 | ||||
| InChIKey | FHQVHHIBKUMWTI-OTMQOFQLSA-N | ||||
| PubChem Compound ID | 59834030 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7W7F Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431 | ||||||
| Method | Electron microscopy | Resolution | 3.35 Å | Mutation | No | [1] |
| PDB Sequence |
PVRKIAIKIL
125 VHSLFSMLIM135 CTILTNCVFM145 TLSNPPDWTK155 NVEYTFTGIY165 TFESLIKILA 175 RGFCLEDFTF185 LRDPWNWLDF195 SVIVMAYVTE205 FVSLVSALRT217 FRVLRALKTI 227 SVIPGLKTIV237 GALIQSVKKL247 SDVMILTVFC257 LSVFALIGLQ267 LFMGNLRNKC 277 LQWPPSFNWK316 DYIGDDSHFY326 VLDGQKDPLL336 CGNGSDAGQC346 PEGYICVKAG 356 RNPNYGYTSF366 DTFSWAFLSL376 FRLMTQDYWE386 NLYQLTLRAA396 GKTYMIFFVL 406 VIFLGSFYLV416 NLILAVVAMA426 YEEQNQATLE436 EADCCDAWLK748 VKHLVNLIVM 758 DPFVDLAITI768 CIVLNTLFMA778 MEHYPMTEQF788 SSVLTVGNLV798 FTGIFTAEMV 808 LKIIAMDPYY818 YFQEGWNIFD828 GIIVSLSLME838 LGLSNVEGLS848 VLRSFRLLRV 858 FKLAKSWPTL868 NMLIKIIGNS878 VGALGNLTLV888 LAIIVFIFAV898 VGMQLFGKSY 908 KECVCKINDD918 CTLPRWHMND928 FFHSFLIVFR938 VLCGEWIETM948 WDCMEVAGQT 958 MCLIVFMLVM968 VIGNLVVLNL978 FLALLLSSFG1189 KIWWNLRKTC1199 YSIVEHNWFE 1209 TFIVFMILLS1219 SGALAFEDIY1229 IEQRKTIKTM1239 LEYADKVFTY1249 IFILEMLLKW 1259 VAYGFQTYFT1269 NAWCWLDFLI1279 VDVSLVSLVA1289 NALGYSELGA1299 IKSLRTLRAL 1309 RPLRALSRFE1319 GMRVVVNALV1329 GAIPSIMNVL1339 LVCLIFWLIF1349 SIMGVNLFAG 1359 KFYHCVNMTT1369 GNMFDISDVN1379 NLSDCQALGK1389 QARWKNVKVN1399 FDNVGAGYLA 1409 LLQVATFKGW1419 MDIMYAAVDS1429 RDVKLQPVYE1439 ENLYMYLYFV1449 IFIIFGSFFT 1459 LNLFIGVIID1469 NFNQQKKKFG1479 GQDIFMTEEQ1489 KKYYNAMKKL1499 GSKKPQKPIP 1509 RPANKFQGMV1519 FDFVTRQVFD1529 ISIMILICLN1539 MVTMMVETDD1549 QGKYMTLVLS 1559 RINLVFIVLF1569 TGEFVLKLVS1579 LRHYYFTIGW1589 NIFDFVVVIL1599 SIVGMFLAEM 1609 IEKYFVSPTL1619 FRVIRLARIG1629 RILRLIKGAK1639 GIRTLLFALM1649 MSLPALFNIG 1659 LLLFLVMFIY1669 AIFGMSNFAY1679 VKKEAGIDDM1689 FNFETFGNSM1699 ICLFQITTSA 1709 GWDGLLAPIL1719 NSAPPDCDPD1729 TIHPGSSVKG1739 DCGNPSVGIF1749 FFVSYIIISF 1759 LVVVNMYIAV1769 ILENFSVAT
|
|||||
|
|
VAL143
4.579
THR146
3.159
LEU147
4.235
SER148
4.002
ILE252
3.733
VAL255
4.136
PHE256
4.176
SER259
4.220
ILE264
4.360
LEU268
4.069
TYR361
4.665
GLY362
3.827
THR368
4.245
PHE369
3.995
SER370
3.521
TRP371
3.106
PHE373
3.615
LEU374
4.066
PHE377
4.540
THR399
3.394
TYR400
3.902
ILE402
4.611
PHE403
3.688
LEU406
3.615
GLY823
4.197
ILE826
4.586
PHE827
4.021
ILE830
3.787
GLY846
4.554
PHE853
4.281
LEU856
4.321
ALA890
4.074
PHE894
3.954
PHE929
4.228
PHE930
3.216
PHE933
3.603
GLN957
3.199
THR958
3.744
LEU961
3.606
ILE962
3.539
MET965
4.158
GLY1221
4.447
ALA1224
3.876
PHE1225
3.545
ASP1227
3.217
ARG1233
3.447
ASN1270
4.691
ALA1271
4.164
TRP1272
3.624
SER1302
3.685
THR1305
3.262
LEU1306
4.504
LEU1312
4.770
LEU1315
4.936
VAL1325
4.421
ASN1326
3.145
VAL1329
4.427
LEU1339
4.909
CYS1342
4.593
LEU1343
3.753
TRP1346
3.519
MET1352
4.556
ASN1402
4.662
GLY1404
3.157
ALA1405
3.587
TYR1407
3.737
LEU1408
3.889
LEU1411
4.258
ASN1441
4.600
TYR1443
3.554
MET1444
4.229
LEU1446
3.914
TYR1447
4.395
ILE1450
3.803
ILE1530
3.659
ILE1534
3.740
CYS1537
3.670
LEU1538
3.665
MET1540
4.756
VAL1541
3.869
THR1542
3.589
MET1544
4.059
VAL1545
4.051
THR1547
3.931
ASP1548
4.971
TYR1553
3.637
MET1554
4.279
VAL1557
4.133
LEU1558
4.752
ILE1561
4.312
VAL1567
4.595
THR1570
4.891
ILE1601
4.278
PHE1605
4.803
THR1618
3.562
LEU1619
4.835
VAL1622
3.721
LEU1625
4.320
LEU1634
4.170
ALA1638
4.249
ILE1641
4.929
PHE1667
4.520
PHE1672
3.560
SER1675
3.946
ASN1676
4.065
PHE1695
3.905
ASN1743
4.500
PRO1744
3.394
SER1745
3.202
VAL1746
4.140
ILE1748
3.821
PHE1749
3.600
VAL1752
3.514
SER1753
4.221
ILE1756
3.721
ILE1757
4.119
|
|||||
| PDB ID: 7W77 cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA | ||||||
| Method | Electron microscopy | Resolution | 3.30 Å | Mutation | No | [1] |
| PDB Sequence |
PVRKIAIKIL
125 VHSLFSMLIM135 CTILTNCVFM145 TLSNPPDWTK155 NVEYTFTGIY165 TFESLIKILA 175 RGFCLEDFTF185 LRDPWNWLDF195 SVIVMAYVTE205 FVSLVSALRT217 FRVLRALKTI 227 SVIPGLKTIV237 GALIQSVKKL247 SDVMILTVFC257 LSVFALIGLQ267 LFMGNLRNKC 277 LQWPPSFNWK316 DYIGDDSHFY326 VLDGQKDPLL336 CGNGSDAGQC346 PEGYICVKAG 356 RNPNYGYTSF366 DTFSWAFLSL376 FRLMTQDYWE386 NLYQLTLRAA396 GKTYMIFFVL 406 VIFLGSFYLV416 NLILAVVAMA426 YEEQNQATLE436 EADCCDAWLK748 VKHLVNLIVM 758 DPFVDLAITI768 CIVLNTLFMA778 MEHYPMTEQF788 SSVLTVGNLV798 FTGIFTAEMV 808 LKIIAMDPYY818 YFQEGWNIFD828 GIIVSLSLME838 LGLSNVEGLS848 VLRSFRLLRV 858 FKLAKSWPTL868 NMLIKIIGNS878 VGALGNLTLV888 LAIIVFIFAV898 VGMQLFGKSY 908 KECVCKINDD918 CTLPRWHMND928 FFHSFLIVFR938 VLCGEWIETM948 WDCMEVAGQT 958 MCLIVFMLVM968 VIGNLVVLNL978 FLALLLSSFG1189 KIWWNLRKTC1199 YSIVEHNWFE 1209 TFIVFMILLS1219 SGALAFEDIY1229 IEQRKTIKTM1239 LEYADKVFTY1249 IFILEMLLKW 1259 VAYGFQTYFT1269 NAWCWLDFLI1279 VDVSLVSLVA1289 NALGYSELGA1299 IKSLRTLRAL 1309 RPLRALSRFE1319 GMRVVVNALV1329 GAIPSIMNVL1339 LVCLIFWLIF1349 SIMGVNLFAG 1359 KFYHCVNMTT1369 GNMFDISDVN1379 NLSDCQALGK1389 QARWKNVKVN1399 FDNVGAGYLA 1409 LLQVATFKGW1419 MDIMYAAVDS1429 RDVKLQPVYE1439 ENLYMYLYFV1449 IFIIFGSFFT 1459 LNLFIGVIID1469 NFNQQKKKFG1479 GQDIFMTEEQ1489 KKYYNAMKKL1499 GSKKPQKPIP 1509 RPANKFQGMV1519 FDFVTRQVFD1529 ISIMILICLN1539 MVTMMVETDD1549 QGKYMTLVLS 1559 RINLVFIVLF1569 TGEFVLKLVS1579 LRHYYFTIGW1589 NIFDFVVVIL1599 SIVGMFLAEM 1609 IEKYFVSPTL1619 FRVIRLARIG1629 RILRLIKGAK1639 GIRTLLFALM1649 MSLPALFNIG 1659 LLLFLVMFIY1669 AIFGMSNFAY1679 VKKEAGIDDM1689 FNFETFGNSM1699 ICLFQITTSA 1709 GWDGLLAPIL1719 NSAPPDCDPD1729 TIHPGSSVKG1739 DCGNPSVGIF1749 FFVSYIIISF 1759 LVVVNMYIAV1769 ILENFSVAT
|
|||||
|
|
CYS142
4.875
VAL143
4.375
THR146
1.491
LEU147
4.594
SER148
4.678
ILE252
3.871
VAL255
3.912
PHE256
4.432
SER259
3.193
ILE264
4.538
LEU268
3.699
TYR361
4.227
GLY362
4.031
TYR363
4.440
THR368
3.980
PHE369
4.077
SER370
3.395
TRP371
1.376
PHE373
3.809
LEU374
3.913
PHE377
4.885
THR399
3.631
TYR400
4.157
ILE402
4.189
PHE403
4.149
LEU406
4.633
GLY823
3.445
ILE826
4.625
PHE827
4.346
ILE830
4.345
LEU847
3.642
VAL849
3.888
LEU856
4.159
ALA890
4.385
ILE891
4.510
VAL893
4.802
PHE894
4.103
PHE929
3.553
PHE930
3.861
PHE933
3.617
GLN957
3.280
THR958
3.469
LEU961
3.669
ILE962
4.095
MET965
3.996
GLY1221
4.432
ALA1224
3.686
PHE1225
3.660
ASP1227
4.039
ARG1233
3.352
ALA1271
3.502
TRP1272
3.082
LEU1275
4.778
SER1302
4.158
THR1305
4.312
LEU1306
4.576
LEU1309
4.160
LEU1312
3.720
LEU1315
4.468
VAL1325
3.900
ASN1326
4.541
VAL1329
4.481
LEU1339
4.619
CYS1342
4.617
LEU1343
3.642
TRP1346
3.730
PHE1349
4.811
MET1352
3.566
LEU1356
4.830
ASN1402
4.843
GLY1404
3.224
ALA1405
3.839
TYR1407
3.682
LEU1408
4.391
LEU1411
3.574
TYR1443
3.100
MET1444
4.162
LEU1446
3.717
TYR1447
4.122
ILE1450
3.691
ILE1530
4.577
MET1533
4.401
ILE1534
3.725
CYS1537
3.975
LEU1538
4.416
MET1540
4.124
VAL1541
3.971
THR1542
4.252
MET1544
3.723
VAL1545
3.661
THR1547
4.095
TYR1553
1.490
MET1554
3.760
VAL1557
4.316
LEU1558
4.992
ILE1561
4.112
THR1618
2.999
VAL1622
3.817
LEU1625
4.420
LEU1634
4.659
ALA1638
4.180
ILE1641
4.352
PHE1667
4.480
PHE1672
4.543
ASN1676
4.401
PHE1695
4.197
LEU1719
4.902
ASN1743
4.116
PRO1744
3.461
SER1745
3.138
VAL1746
4.197
ILE1748
3.414
PHE1749
4.252
VAL1752
3.671
SER1753
4.115
ILE1756
3.662
ILE1757
4.551
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for modulation of human Na(V)1.3 by clinical drug and selective antagonist. Nat Commun. 2022 Mar 11;13(1):1286. | ||||
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