Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T56057 | Target Info | |||
| Target Name | Lysine-specific demethylase 6B (KDM6B) | ||||
| Synonyms | Lysine demethylase 6B; KIAA0346; Jumonji domain-containing protein 3; JmjC domain-containing protein 3; JMJD3 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | KDM6B | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 2-Methyl-2-Propanol | Ligand Info | |||||
| Structure Description | The catalytic domain of KDM6B in complex with H3(17-33)K18IA21M peptide | PDB:6F6D | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [1] |
| PDB Sequence |
ESYLSPAQSV
1166 KPKINTEEKL1176 PREKLNPPTP1186 SIYLESKRDA1196 FSPVLLQFCT1206 DPRNPITVIR 1216 GLAGSLRLNL1226 GLFSTKTLVE1236 ASGEHTVEVR1246 TQVQQPSDEN1256 WDLTGTRQIW 1266 PCESSRSHTT1276 IAKYAQYQAS1286 SFQESHIIKF1328 GTNIDLSDAK1338 RWKPQLQELL 1348 KLPAFMRVTS1358 TGNMLSHVGH1368 TILGMNTVQL1378 YMKVPGSRTP1388 GHQENNNFCS 1398 VNINIGPGDC1408 EWFAVHEHYW1418 ETISAFCDRH1428 GVDYLTGSWW1438 PILDDLYASN 1448 IPVYRFVQRP1458 GDLVWINAGT1468 VHWVQATGWC1478 NNIAWNVGPL1488 TAYQYQLALE 1498 RYEWNEVKNV1508 KSIVPMIHVS1518 WNVARTVKIS1528 DPDLFKMIKF1538 CLLQSMKHCQ 1548 VQRESLVRAG1558 KKIAYQGRVK1568 DEPAYYCNEC1578 DVEVFNILFV1588 TSENGSRNTY 1598 LVHCEGCARR1608 RSAGLQGVVV1618 LEQYRTEELA1628 QAYDAFTLAP1638 |
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ILE1188
2.726
TYR1189
4.703
LEU1190
2.736
ASP1195
3.458
ALA1196
4.900
SER1198
3.432
VAL1200
2.537
LEU1201
2.395
PHE1204
2.897
THR1231
3.082
THR1242
2.614
VAL1243
2.458
GLU1244
2.536
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Alpha-ketoglutaric acid | Ligand Info | |||||
| Structure Description | The catalytic domain of KDM6B in complex with H3(17-33)K18IA21M peptide | PDB:6F6D | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [1] |
| PDB Sequence |
ESYLSPAQSV
1166 KPKINTEEKL1176 PREKLNPPTP1186 SIYLESKRDA1196 FSPVLLQFCT1206 DPRNPITVIR 1216 GLAGSLRLNL1226 GLFSTKTLVE1236 ASGEHTVEVR1246 TQVQQPSDEN1256 WDLTGTRQIW 1266 PCESSRSHTT1276 IAKYAQYQAS1286 SFQESHIIKF1328 GTNIDLSDAK1338 RWKPQLQELL 1348 KLPAFMRVTS1358 TGNMLSHVGH1368 TILGMNTVQL1378 YMKVPGSRTP1388 GHQENNNFCS 1398 VNINIGPGDC1408 EWFAVHEHYW1418 ETISAFCDRH1428 GVDYLTGSWW1438 PILDDLYASN 1448 IPVYRFVQRP1458 GDLVWINAGT1468 VHWVQATGWC1478 NNIAWNVGPL1488 TAYQYQLALE 1498 RYEWNEVKNV1508 KSIVPMIHVS1518 WNVARTVKIS1528 DPDLFKMIKF1538 CLLQSMKHCQ 1548 VQRESLVRAG1558 KKIAYQGRVK1568 DEPAYYCNEC1578 DVEVFNILFV1588 TSENGSRNTY 1598 LVHCEGCARR1608 RSAGLQGVVV1618 LEQYRTEELA1628 QAYDAFTLAP1638 |
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: GSK-J1 | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF JMJD3 WITH GSK-J1 | PDB:4ASK | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [2] |
| PDB Sequence |
PREKLNPPTP
1186 SIYLESKRDA1196 FSPVLLQFCT1206 DPRNPITVIR1216 GLAGSLRLNL1226 GLFSTKTLVE 1236 ASGEHTVEVR1246 TQVQQPSDEN1256 WDLTGTRQIW1266 PCESSRSHTT1276 IAKYAQYQAS 1286 SFQESLHHII1326 KFGTNIDLSD1336 AKRWKPQLQE1346 LLKLPAFMRV1356 TSTGNMLSHV 1366 GHTILGMNTV1376 QLYMKVPGSR1386 TPGHQENNNF1396 CSVNINIGPG1406 DCEWFAVHEH 1416 YWETISAFCD1426 RHGVDYLTGS1436 WWPILDDLYA1446 SNIPVYRFVQ1456 RPGDLVWINA 1466 GTVHWVQATG1476 WCNNIAWNVG1486 PLTAYQYQLA1496 LERYEWNEVK1506 NVKSIVPMIH 1516 VSWNVARTVK1526 ISDPDLFKMI1536 KFCLLQSMKH1546 CQVQRESLVR1556 AGKKIAYQGR 1566 VKDEPAYYCN1576 ECDVEVFNIL1586 FVTSENTYLV1600 HCEGCARRRS1610 AGLQGVVVLE 1620 QYRTEELAQA1630 YDAFTLAP
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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 .K0I or .K0I2 or .K0I3 or :3K0I;style chemicals stick;color identity;select .A:1246 or .A:1248 or .A:1270 or .A:1328 or .A:1330 or .A:1331 or .A:1379 or .A:1381 or .A:1386 or .A:1387 or .A:1388 or .A:1390 or .A:1391 or .A:1392 or .A:1393 or .A:1400 or .A:1410 or .A:1436 or .A:1472 or .A:1480; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1246
3.469
GLN1248
3.824
SER1270
3.641
PHE1328
3.853
THR1330
3.529
ASN1331
3.524
TYR1379
3.617
LYS1381
2.690
ARG1386
3.543
THR1387
2.636
|
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| Ligand Name: Hydroxyqunoline analog 1 | Ligand Info | |||||
| Structure Description | Crystal structure of the human JMJD3 jumonji domain | PDB:2XXZ | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [3] |
| PDB Sequence |
REKLNPPTPS
1184 IYLESKRDAF1194 SPVLLQFCTD1204 PRNPITVIRG1214 LAGSLRLNLG1224 LFSTKTLVEA 1234 SGEHTVEVRT1244 QVQQPSDENW1254 DLTGTRQIWP1264 CESSRSHTTI1274 AKYAQYQASS 1284 FQESLQEEHH1321 IIKFGTNIDL1331 SDAKRWKPQL1341 QELLKLPAFM1351 RVTSTGNMLS 1361 HVGHTILGMN1371 TVQLYMKVPG1381 SRTPGHQENN1391 NFCSVNINIG1401 PGDCEWFAVH 1411 EHYWETISAF1421 CDRHGVDYLT1431 GSWWPILDDL1441 YASNIPVYRF1451 VQRPGDLVWI 1461 NAGTVHWVQA1471 TGWCNNIAWN1481 VGPLTAYQYQ1491 LA
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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 .8XQ or .8XQ2 or .8XQ3 or :38XQ;style chemicals stick;color identity;select .A:1325 or .A:1327 or .A:1328 or .A:1376 or .A:1378 or .A:1384 or .A:1387 or .A:1389 or .A:1395 or .A:1397 or .A:1407 or .A:1461 or .A:1467 or .A:1469 or .A:1477; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(4-Phenylbutanoylamino)pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases | PDB:5FP3 | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [4] |
| PDB Sequence |
PREKLNPPTP
1186 SIYLESKRDA1196 FSPVLLQFCT1206 DPRNPITVIR1216 GLAGSLRLNL1226 GLFSTKTLVE 1236 ASGEHTVEVR1246 TQVQQPSDEN1256 WDLTGTRQIW1266 PCESSRSHTT1276 IAKYAQYQAS 1286 SFQESLPKNH1323 HIIKFGTNID1333 LSDAKRWKPQ1343 LQELLKLPAF1353 MRVTSTGNML 1363 SHVGHTILGM1373 NTVQLYMKVP1383 GSRTPGHQEN1393 NNFCSVNINI1403 GPGDCEWFAV 1413 HEHYWETISA1423 FCDRHGVDYL1433 TGSWWPILDD1443 LYASNIPVYR1453 FVQRPGDLVW 1463 INAGTVHWVQ1473 ATGWCNNIAW1483 NVGPLTAYQY1493 QLALERYEWN1503 EVKNVKSIVP 1513 MIHVSWNVAR1523 TVKISDPDLF1533 KMIKFCLLQS1543 MKHCQVQRES1553 LVRAGKKIAY 1563 QGRVKDEPAY1573 YCNECDVEVF1583 NILFVTSENG1593 SRNTYLVHCE1603 GCARRRSAGL 1613 QGVVVLEQYR1623 TEELAQAYDA1633 FTLAP
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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 .YC8 or .YC82 or .YC83 or :3YC8;style chemicals stick;color identity;select .A:1246 or .A:1248 or .A:1270 or .A:1328 or .A:1330 or .A:1331 or .A:1379 or .A:1381 or .A:1386 or .A:1387 or .A:1388 or .A:1390 or .A:1392 or .A:1400 or .A:1410 or .A:1436 or .A:1470 or .A:1472 or .A:1480; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1246
3.507
GLN1248
3.538
SER1270
3.873
PHE1328
3.761
THR1330
3.125
ASN1331
4.204
TYR1379
3.413
LYS1381
2.796
ARG1386
3.480
THR1387
2.715
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity. Biochemistry. 2018 Feb 6;57(5):585-592. | ||||
| REF 2 | A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature. 2012 Aug 16;488(7411):404-8. | ||||
| REF 3 | Crystal Structure of the Human Jmjd3 Jumonji Domain | ||||
| REF 4 | Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-pyridine Carboxylate Derivatives. J Med Chem. 2016 Feb 25;59(4):1357-69. | ||||
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