Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
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
SCN3A_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Bulleyaconitine A Ligand Info
Structure Description cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA PDB:7W77
Method Electron microscopy Resolution 3.30 Å Mutation No [1]
PDB Sequence
PVRKIAIKIL
125
VHSLFSMLIM
135
CTILTNCVFM
145
TLSNPPDWTK
155
NVEYTFTGIY
165

TFESLIKILA
175
RGFCLEDFTF
185
LRDPWNWLDF
195
SVIVMAYVTE
205
FVSLVSALRT
217

FRVLRALKTI
227
SVIPGLKTIV
237
GALIQSVKKL
247
SDVMILTVFC
257
LSVFALIGLQ
267

LFMGNLRNKC
277
LQWPPSFNWK
316
DYIGDDSHFY
326
VLDGQKDPLL
336
CGNGSDAGQC
346

PEGYICVKAG
356
RNPNYGYTSF
366
DTFSWAFLSL
376
FRLMTQDYWE
386
NLYQLTLRAA
396

GKTYMIFFVL
406
VIFLGSFYLV
416
NLILAVVAMA
426
YEEQNQATLE
436
EADCCDAWLK
748

VKHLVNLIVM
758
DPFVDLAITI
768
CIVLNTLFMA
778
MEHYPMTEQF
788
SSVLTVGNLV
798

FTGIFTAEMV
808
LKIIAMDPYY
818
YFQEGWNIFD
828
GIIVSLSLME
838
LGLSNVEGLS
848

VLRSFRLLRV
858
FKLAKSWPTL
868
NMLIKIIGNS
878
VGALGNLTLV
888
LAIIVFIFAV
898

VGMQLFGKSY
908
KECVCKINDD
918
CTLPRWHMND
928
FFHSFLIVFR
938
VLCGEWIETM
948

WDCMEVAGQT
958
MCLIVFMLVM
968
VIGNLVVLNL
978
FLALLLSSFG
1189
KIWWNLRKTC
1199

YSIVEHNWFE
1209
TFIVFMILLS
1219
SGALAFEDIY
1229
IEQRKTIKTM
1239
LEYADKVFTY
1249

IFILEMLLKW
1259
VAYGFQTYFT
1269
NAWCWLDFLI
1279
VDVSLVSLVA
1289
NALGYSELGA
1299

IKSLRTLRAL
1309
RPLRALSRFE
1319
GMRVVVNALV
1329
GAIPSIMNVL
1339
LVCLIFWLIF
1349

SIMGVNLFAG
1359
KFYHCVNMTT
1369
GNMFDISDVN
1379
NLSDCQALGK
1389
QARWKNVKVN
1399

FDNVGAGYLA
1409
LLQVATFKGW
1419
MDIMYAAVDS
1429
RDVKLQPVYE
1439
ENLYMYLYFV
1449

IFIIFGSFFT
1459
LNLFIGVIID
1469
NFNQQKKKFG
1479
GQDIFMTEEQ
1489
KKYYNAMKKL
1499

GSKKPQKPIP
1509
RPANKFQGMV
1519
FDFVTRQVFD
1529
ISIMILICLN
1539
MVTMMVETDD
1549

QGKYMTLVLS
1559
RINLVFIVLF
1569
TGEFVLKLVS
1579
LRHYYFTIGW
1589
NIFDFVVVIL
1599

SIVGMFLAEM
1609
IEKYFVSPTL
1619
FRVIRLARIG
1629
RILRLIKGAK
1639
GIRTLLFALM
1649

MSLPALFNIG
1659
LLLFLVMFIY
1669
AIFGMSNFAY
1679
VKKEAGIDDM
1689
FNFETFGNSM
1699

ICLFQITTSA
1709
GWDGLLAPIL
1719
NSAPPDCDPD
1729
TIHPGSSVKG
1739
DCGNPSVGIF
1749

FFVSYIIISF
1759
LVVVNMYIAV
1769
ILENFSVAT
Residue
Distance (Å)
MET251
4.743
THR254
4.556
PHE377
3.896
MET380
3.578
THR381
2.614
GLN382
4.248
ASP383
4.521
SER412
3.690
VAL416
1.491
ILE419
3.786
LEU420
3.624
VAL939
4.415
LEU940
3.594
CYS941
2.779
Residue
Distance (Å)
GLY942
3.119
GLU943
4.954
TRP944
4.083
MET968
3.144
VAL969
4.672
ASN972
1.297
VAL975
4.693
LEU976
4.093
PHE979
3.451
PHE1416
3.680
PHE1457
4.969
LEU1460
4.792
TYR1766
4.045
Ligand Name: 2,2-diphenyl-N-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]acetamide Ligand Info
Structure Description Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431 PDB:7W7F
Method Electron microscopy Resolution 3.35 Å Mutation No [1]
PDB Sequence
PVRKIAIKIL
125
VHSLFSMLIM
135
CTILTNCVFM
145
TLSNPPDWTK
155
NVEYTFTGIY
165

TFESLIKILA
175
RGFCLEDFTF
185
LRDPWNWLDF
195
SVIVMAYVTE
205
FVSLVSALRT
217

FRVLRALKTI
227
SVIPGLKTIV
237
GALIQSVKKL
247
SDVMILTVFC
257
LSVFALIGLQ
267

LFMGNLRNKC
277
LQWPPSFNWK
316
DYIGDDSHFY
326
VLDGQKDPLL
336
CGNGSDAGQC
346

PEGYICVKAG
356
RNPNYGYTSF
366
DTFSWAFLSL
376
FRLMTQDYWE
386
NLYQLTLRAA
396

GKTYMIFFVL
406
VIFLGSFYLV
416
NLILAVVAMA
426
YEEQNQATLE
436
EADCCDAWLK
748

VKHLVNLIVM
758
DPFVDLAITI
768
CIVLNTLFMA
778
MEHYPMTEQF
788
SSVLTVGNLV
798

FTGIFTAEMV
808
LKIIAMDPYY
818
YFQEGWNIFD
828
GIIVSLSLME
838
LGLSNVEGLS
848

VLRSFRLLRV
858
FKLAKSWPTL
868
NMLIKIIGNS
878
VGALGNLTLV
888
LAIIVFIFAV
898

VGMQLFGKSY
908
KECVCKINDD
918
CTLPRWHMND
928
FFHSFLIVFR
938
VLCGEWIETM
948

WDCMEVAGQT
958
MCLIVFMLVM
968
VIGNLVVLNL
978
FLALLLSSFG
1189
KIWWNLRKTC
1199

YSIVEHNWFE
1209
TFIVFMILLS
1219
SGALAFEDIY
1229
IEQRKTIKTM
1239
LEYADKVFTY
1249

IFILEMLLKW
1259
VAYGFQTYFT
1269
NAWCWLDFLI
1279
VDVSLVSLVA
1289
NALGYSELGA
1299

IKSLRTLRAL
1309
RPLRALSRFE
1319
GMRVVVNALV
1329
GAIPSIMNVL
1339
LVCLIFWLIF
1349

SIMGVNLFAG
1359
KFYHCVNMTT
1369
GNMFDISDVN
1379
NLSDCQALGK
1389
QARWKNVKVN
1399

FDNVGAGYLA
1409
LLQVATFKGW
1419
MDIMYAAVDS
1429
RDVKLQPVYE
1439
ENLYMYLYFV
1449

IFIIFGSFFT
1459
LNLFIGVIID
1469
NFNQQKKKFG
1479
GQDIFMTEEQ
1489
KKYYNAMKKL
1499

GSKKPQKPIP
1509
RPANKFQGMV
1519
FDFVTRQVFD
1529
ISIMILICLN
1539
MVTMMVETDD
1549

QGKYMTLVLS
1559
RINLVFIVLF
1569
TGEFVLKLVS
1579
LRHYYFTIGW
1589
NIFDFVVVIL
1599

SIVGMFLAEM
1609
IEKYFVSPTL
1619
FRVIRLARIG
1629
RILRLIKGAK
1639
GIRTLLFALM
1649

MSLPALFNIG
1659
LLLFLVMFIY
1669
AIFGMSNFAY
1679
VKKEAGIDDM
1689
FNFETFGNSM
1699

ICLFQITTSA
1709
GWDGLLAPIL
1719
NSAPPDCDPD
1729
TIHPGSSVKG
1739
DCGNPSVGIF
1749

FFVSYIIISF
1759
LVVVNMYIAV
1769
ILENFSVAT
Residue
Distance (Å)
LEU1556
4.586
LEU1558
4.686
SER1559
3.469
ASN1562
2.179
LEU1563
3.500
SER1600
3.720
GLY1603
3.818
MET1604
3.389
PHE1605
4.854
Residue
Distance (Å)
ALA1607
4.085
GLU1608
3.445
PHE1620
4.759
ILE1623
4.998
ARG1624
2.991
ALA1626
4.235
ARG1627
3.951
ARG1630
3.018
Ligand Name: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en Ligand Info
Structure Description cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA PDB:7W77
Method Electron microscopy Resolution 3.30 Å Mutation No [1]
PDB Sequence
PVRKIAIKIL
125
VHSLFSMLIM
135
CTILTNCVFM
145
TLSNPPDWTK
155
NVEYTFTGIY
165

TFESLIKILA
175
RGFCLEDFTF
185
LRDPWNWLDF
195
SVIVMAYVTE
205
FVSLVSALRT
217

FRVLRALKTI
227
SVIPGLKTIV
237
GALIQSVKKL
247
SDVMILTVFC
257
LSVFALIGLQ
267

LFMGNLRNKC
277
LQWPPSFNWK
316
DYIGDDSHFY
326
VLDGQKDPLL
336
CGNGSDAGQC
346

PEGYICVKAG
356
RNPNYGYTSF
366
DTFSWAFLSL
376
FRLMTQDYWE
386
NLYQLTLRAA
396

GKTYMIFFVL
406
VIFLGSFYLV
416
NLILAVVAMA
426
YEEQNQATLE
436
EADCCDAWLK
748

VKHLVNLIVM
758
DPFVDLAITI
768
CIVLNTLFMA
778
MEHYPMTEQF
788
SSVLTVGNLV
798

FTGIFTAEMV
808
LKIIAMDPYY
818
YFQEGWNIFD
828
GIIVSLSLME
838
LGLSNVEGLS
848

VLRSFRLLRV
858
FKLAKSWPTL
868
NMLIKIIGNS
878
VGALGNLTLV
888
LAIIVFIFAV
898

VGMQLFGKSY
908
KECVCKINDD
918
CTLPRWHMND
928
FFHSFLIVFR
938
VLCGEWIETM
948

WDCMEVAGQT
958
MCLIVFMLVM
968
VIGNLVVLNL
978
FLALLLSSFG
1189
KIWWNLRKTC
1199

YSIVEHNWFE
1209
TFIVFMILLS
1219
SGALAFEDIY
1229
IEQRKTIKTM
1239
LEYADKVFTY
1249

IFILEMLLKW
1259
VAYGFQTYFT
1269
NAWCWLDFLI
1279
VDVSLVSLVA
1289
NALGYSELGA
1299

IKSLRTLRAL
1309
RPLRALSRFE
1319
GMRVVVNALV
1329
GAIPSIMNVL
1339
LVCLIFWLIF
1349

SIMGVNLFAG
1359
KFYHCVNMTT
1369
GNMFDISDVN
1379
NLSDCQALGK
1389
QARWKNVKVN
1399

FDNVGAGYLA
1409
LLQVATFKGW
1419
MDIMYAAVDS
1429
RDVKLQPVYE
1439
ENLYMYLYFV
1449

IFIIFGSFFT
1459
LNLFIGVIID
1469
NFNQQKKKFG
1479
GQDIFMTEEQ
1489
KKYYNAMKKL
1499

GSKKPQKPIP
1509
RPANKFQGMV
1519
FDFVTRQVFD
1529
ISIMILICLN
1539
MVTMMVETDD
1549

QGKYMTLVLS
1559
RINLVFIVLF
1569
TGEFVLKLVS
1579
LRHYYFTIGW
1589
NIFDFVVVIL
1599

SIVGMFLAEM
1609
IEKYFVSPTL
1619
FRVIRLARIG
1629
RILRLIKGAK
1639
GIRTLLFALM
1649

MSLPALFNIG
1659
LLLFLVMFIY
1669
AIFGMSNFAY
1679
VKKEAGIDDM
1689
FNFETFGNSM
1699

ICLFQITTSA
1709
GWDGLLAPIL
1719
NSAPPDCDPD
1729
TIHPGSSVKG
1739
DCGNPSVGIF
1749

FFVSYIIISF
1759
LVVVNMYIAV
1769
ILENFSVAT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9Z9 or .9Z92 or .9Z93 or :39Z9;style chemicals stick;color identity;select .D:342 or .D:398 or .D:399 or .D:401 or .D:402 or .D:405 or .D:767 or .D:771 or .D:775 or .D:778 or .D:779 or .D:781 or .D:782 or .D:783 or .D:861 or .D:864 or .D:865 or .D:866 or .D:1337 or .D:1340 or .D:1344 or .D:1347 or .D:1402 or .D:1403 or .D:1404 or .D:1407 or .D:1659 or .D:1663 or .D:1666 or .D:1696 or .D:1699 or .D:1700 or .D:1703; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP342
3.840
LYS398
4.278
THR399
4.367
MET401
3.521
ILE402
3.723
VAL405
3.830
THR767
4.874
VAL771
3.631
LEU775
3.992
ALA778
4.030
MET779
4.694
HIS781
3.370
TYR782
4.299
PRO783
3.917
LEU861
3.886
SER864
3.201
TRP865
3.469
Residue
Distance (Å)
PRO866
3.701
ASN1337
4.924
LEU1340
3.751
ILE1344
3.542
LEU1347
4.023
ASN1402
3.555
VAL1403
3.700
GLY1404
4.111
TYR1407
4.088
GLY1659
4.530
PHE1663
4.107
MET1666
3.621
GLY1696
3.879
MET1699
3.383
ILE1700
4.713
PHE1703
3.781
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine Ligand Info
Structure Description cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA PDB:7W77
Method Electron microscopy Resolution 3.30 Å Mutation No [1]
PDB Sequence
PVRKIAIKIL
125
VHSLFSMLIM
135
CTILTNCVFM
145
TLSNPPDWTK
155
NVEYTFTGIY
165

TFESLIKILA
175
RGFCLEDFTF
185
LRDPWNWLDF
195
SVIVMAYVTE
205
FVSLVSALRT
217

FRVLRALKTI
227
SVIPGLKTIV
237
GALIQSVKKL
247
SDVMILTVFC
257
LSVFALIGLQ
267

LFMGNLRNKC
277
LQWPPSFNWK
316
DYIGDDSHFY
326
VLDGQKDPLL
336
CGNGSDAGQC
346

PEGYICVKAG
356
RNPNYGYTSF
366
DTFSWAFLSL
376
FRLMTQDYWE
386
NLYQLTLRAA
396

GKTYMIFFVL
406
VIFLGSFYLV
416
NLILAVVAMA
426
YEEQNQATLE
436
EADCCDAWLK
748

VKHLVNLIVM
758
DPFVDLAITI
768
CIVLNTLFMA
778
MEHYPMTEQF
788
SSVLTVGNLV
798

FTGIFTAEMV
808
LKIIAMDPYY
818
YFQEGWNIFD
828
GIIVSLSLME
838
LGLSNVEGLS
848

VLRSFRLLRV
858
FKLAKSWPTL
868
NMLIKIIGNS
878
VGALGNLTLV
888
LAIIVFIFAV
898

VGMQLFGKSY
908
KECVCKINDD
918
CTLPRWHMND
928
FFHSFLIVFR
938
VLCGEWIETM
948

WDCMEVAGQT
958
MCLIVFMLVM
968
VIGNLVVLNL
978
FLALLLSSFG
1189
KIWWNLRKTC
1199

YSIVEHNWFE
1209
TFIVFMILLS
1219
SGALAFEDIY
1229
IEQRKTIKTM
1239
LEYADKVFTY
1249

IFILEMLLKW
1259
VAYGFQTYFT
1269
NAWCWLDFLI
1279
VDVSLVSLVA
1289
NALGYSELGA
1299

IKSLRTLRAL
1309
RPLRALSRFE
1319
GMRVVVNALV
1329
GAIPSIMNVL
1339
LVCLIFWLIF
1349

SIMGVNLFAG
1359
KFYHCVNMTT
1369
GNMFDISDVN
1379
NLSDCQALGK
1389
QARWKNVKVN
1399

FDNVGAGYLA
1409
LLQVATFKGW
1419
MDIMYAAVDS
1429
RDVKLQPVYE
1439
ENLYMYLYFV
1449

IFIIFGSFFT
1459
LNLFIGVIID
1469
NFNQQKKKFG
1479
GQDIFMTEEQ
1489
KKYYNAMKKL
1499

GSKKPQKPIP
1509
RPANKFQGMV
1519
FDFVTRQVFD
1529
ISIMILICLN
1539
MVTMMVETDD
1549

QGKYMTLVLS
1559
RINLVFIVLF
1569
TGEFVLKLVS
1579
LRHYYFTIGW
1589
NIFDFVVVIL
1599

SIVGMFLAEM
1609
IEKYFVSPTL
1619
FRVIRLARIG
1629
RILRLIKGAK
1639
GIRTLLFALM
1649

MSLPALFNIG
1659
LLLFLVMFIY
1669
AIFGMSNFAY
1679
VKKEAGIDDM
1689
FNFETFGNSM
1699

ICLFQITTSA
1709
GWDGLLAPIL
1719
NSAPPDCDPD
1729
TIHPGSSVKG
1739
DCGNPSVGIF
1749

FFVSYIIISF
1759
LVVVNMYIAV
1769
ILENFSVAT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6OU or .6OU2 or .6OU3 or :36OU;style chemicals stick;color identity;select .D:142 or .D:143 or .D:146 or .D:147 or .D:148 or .D:252 or .D:255 or .D:256 or .D:259 or .D:264 or .D:268 or .D:361 or .D:362 or .D:363 or .D:368 or .D:369 or .D:370 or .D:371 or .D:373 or .D:374 or .D:377 or .D:399 or .D:400 or .D:402 or .D:403 or .D:406 or .D:823 or .D:826 or .D:827 or .D:830 or .D:847 or .D:849 or .D:856 or .D:890 or .D:891 or .D:893 or .D:894 or .D:929 or .D:930 or .D:933 or .D:957 or .D:958 or .D:961 or .D:962 or .D:965 or .D:1221 or .D:1224 or .D:1225 or .D:1227 or .D:1233 or .D:1271 or .D:1272 or .D:1275 or .D:1302 or .D:1305 or .D:1306 or .D:1309 or .D:1312 or .D:1315 or .D:1325 or .D:1326 or .D:1329 or .D:1339 or .D:1342 or .D:1343 or .D:1346 or .D:1349 or .D:1352 or .D:1356 or .D:1402 or .D:1404 or .D:1405 or .D:1407 or .D:1408 or .D:1411 or .D:1443 or .D:1444 or .D:1446 or .D:1447 or .D:1450 or .D:1530 or .D:1533 or .D:1534 or .D:1537 or .D:1538 or .D:1540 or .D:1541 or .D:1542 or .D:1544 or .D:1545 or .D:1547 or .D:1553 or .D:1554 or .D:1557 or .D:1558 or .D:1561 or .D:1618 or .D:1622 or .D:1625 or .D:1634 or .D:1638 or .D:1641 or .D:1667 or .D:1672 or .D:1676 or .D:1695 or .D:1719 or .D:1743 or .D:1744 or .D:1745 or .D:1746 or .D:1748 or .D:1749 or .D:1752 or .D:1753 or .D:1756 or .D:1757; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
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
Residue
Distance (Å)
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
Click to View More Binding Site Information of This Target and Ligand Pair
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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