Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Alpha-ketoglutaric acid | Ligand Info | |||
| Canonical SMILES | C(CC(=O)O)C(=O)C(=O)O | ||||
| InChI | 1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10) | ||||
| InChIKey | KPGXRSRHYNQIFN-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 51 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6F6D The catalytic domain of KDM6B in complex with H3(17-33)K18IA21M peptide | ||||||
| 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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| PDB ID: 2XUE CRYSTAL STRUCTURE OF JMJD3 | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
REKLNPPTPS
1187 IYLESKRDAF1197 SPVLLQFCTD1207 PRNPITVIRG1217 LAGSLRLNLG1227 LFSTKTLVEA 1237 SGEHTVEVRT1247 QVQQPSDENW1257 DLTGTRQIWP1267 CESSRSHTTI1277 AKYAQYQASS 1287 FQESLHIIKF1328 GTNIDLSDAK1338 RWKPQLQELL1348 KLPAFMRVTS1358 TGNMLSHVGH 1368 TILGMNTVQL1378 YMKVPGSRTP1388 GHQENNNFCS1398 VNINIGPGDC1408 EWFAVHEHYW 1418 ETISAFCDRH1428 GVDYLTGSWW1438 PILDDLYASN1448 IPVYRFVQRP1458 GDLVWINAGT 1468 VHWVQATGWC1478 NNIAWNVGPL1488 TAYQYQLALE1498 RYEWNEVKNV1508 KSIVPMIHVS 1518 WNVARTVKIS1528 DPDLFKMIKF1538 CLLQSMKHCQ1548 VQRESLVRAG1558 KKIAYQGRVK 1568 DEPAYYCNEC1578 DVEVFNILFV1588 TSENNTYLVH1601 CEGCARRRSA1611 GLQGVVVLEQ 1621 YRTEELAQAY1631 DAFTLAP
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| PDB ID: 5OY3 The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity | ||||||
| Method | X-ray diffraction | Resolution | 2.14 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 TSEGSRNTYL 1599 VHCEGCARRR1609 SAGLQGVVVL1619 EQYRTEELAQ1629 AYDAFTLAPA1639 |
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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. | ||||
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