Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T73551 Target Info
Target Name Lysine N-methyltransferase 3A (SETD2)
Synonyms p231HBP; hSET2; SET2; SET domain-containing protein 2; Protein-lysine N-methyltransferase SETD2; KMT3A; KIAA1732; Huntingtin-interacting protein B; Huntingtin-interacting protein 1; Huntingtin yeast partner B; Histone-lysine N-methyltransferase SETD2; HYPB; HSPC069; HIP-1; HIF1
Target Type Literature-reported Target
Gene Name SETD2
Biochemical Class Methyltransferase
UniProt ID
SETD2_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Ademetionine Ligand Info
Structure Description Crystal Structure of SETD2 bound to Compound 35 PDB:7LZD
Method X-ray diffraction Resolution 1.80 Å Mutation No [1]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
RMQCECTPLS
1505

KDERAQGEIA
1515
CGEDCLNRLL
1525
MIECSSRCPN
1535
GDYCSNRRFQ
1545
RKQHADVEVI
1555

LTEKKGWGLR
1565
AAKDLPSNTF
1575
VLEYCGEVLD
1585
HKEFKARVKE
1595
YARNKNIHYY
1605

FMALKNDEII
1615
DATQKGNCSR
1625
FMNHSCEPNC
1635
ETQKWTVNGQ
1645
LRVGFFTTKL
1655

VPSGSELTFD
1665
YQFQRYGKEA
1675
QKCFCGSANC
1685
RGYLGGE
Residue
Distance (Å)
LYS1559
4.836
LYS1560
2.704
GLY1561
3.534
TRP1562
2.717
GLY1563
4.949
TYR1579
4.334
ILE1602
3.695
HIS1603
2.653
TYR1604
2.874
TYR1605
2.667
ARG1625
3.165
Residue
Distance (Å)
PHE1626
3.616
MET1627
3.661
ASN1628
2.804
HIS1629
2.833
SER1630
4.782
GLN1676
2.609
LYS1677
3.285
CYS1678
3.392
PHE1679
2.858
CYS1680
3.867
LEU1689
3.647
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Sinefungin Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LT8
Method X-ray diffraction Resolution 1.57 Å Mutation No [2]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
KQCECTPLSK
1506

DERAQGEIAC
1516
GEDCLNRLLM
1526
IECSSRCPNG
1536
DYCSNRRFQR
1546
KQHADVEVIL
1556

TEKKGWGLRA
1566
AKDLPSNTFV
1576
LEYCGEVLDH
1586
KEFKARVKEY
1596
ARNKNIHYYF
1606

MALKNDEIID
1616
ATQKGNCSRF
1626
MNHSCEPNCE
1636
TQKWTVNGQL
1646
RVGFFTTKLV
1656

PSGSELTFDY
1666
QAQKCFCGSA
1683
NCRGYLG
Residue
Distance (Å)
LYS1559
4.559
LYS1560
2.021
GLY1561
3.066
TRP1562
2.250
GLY1563
4.413
TYR1579
4.625
ILE1602
3.037
HIS1603
2.411
TYR1604
2.070
TYR1605
2.618
ARG1625
1.995
PHE1626
2.809
Residue
Distance (Å)
MET1627
3.056
ASN1628
2.084
HIS1629
2.021
SER1630
4.030
TYR1666
2.311
GLN1676
2.801
LYS1677
2.813
CYS1678
2.838
PHE1679
2.819
CYS1680
2.954
LEU1689
3.230
Ligand Name: [(2~{s},5~{r})-1-[(2~{r},3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-3,4-Bis(Oxidanyl)oxolan-2-Yl]-5-Azaniumyl-6-Oxidanyl-6-Oxidanylidene-Hexan-2-Yl]-[(2~{r})-2-Oxidanylpropyl]azanium Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LT7
Method X-ray diffraction Resolution 1.51 Å Mutation No [2]
PDB Sequence
GETSVPPGSA
1443
LVGPSCVMDD
1453
FRDPQRWKEC
1463
AKQGKMPCYF
1473
DLIEENVYLM
1497

QCECTPLIAC
1516
GEDCLNRLLM
1526
IECSSRCPNG
1536
DYCSNRRFQR
1546
KQHADVEVIL
1556

TEKKGWGLRA
1566
AKDLPSNTFV
1576
LEYCGEVLDH
1586
KEFKARVKEY
1596
ARNKNIHYYF
1606

MALKNDEIID
1616
ATQKGNCSRF
1626
MNHSCEPNCE
1636
TQKWTVNGQL
1646
RVGFFTTKLV
1656

PSGSELTFDY
1666
QFQRYGKEAQ
1676
KCFCGSANCR
1686
GYLGGENRVS
1696
IRA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .76L or .76L2 or .76L3 or :376L;style chemicals stick;color identity;select .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1602 or .A:1603 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1669 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS1560
2.122
GLY1561
3.055
TRP1562
1.911
GLY1563
4.111
TYR1579
2.488
ILE1602
2.797
HIS1603
2.664
TYR1604
2.473
TYR1605
2.662
PHE1606
4.302
MET1607
4.134
SER1624
2.622
ARG1625
2.054
PHE1626
3.041
Residue
Distance (Å)
MET1627
1.948
ASN1628
2.033
HIS1629
2.074
SER1630
4.152
PHE1650
3.315
PHE1664
2.906
TYR1666
3.145
GLN1669
2.649
GLN1676
3.203
LYS1677
2.746
CYS1678
2.703
PHE1679
3.009
CYS1680
2.905
LEU1689
4.246
Ligand Name: [(2~{s},5~{r})-1-[(2~{r},3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-3,4-Bis(Oxidanyl)oxolan-2-Yl]-5-Azaniumyl-6-Oxidanyl-6-Oxidanylidene-Hexan-2-Yl]-(2-Methylpropyl)azanium Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LSY
Method X-ray diffraction Resolution 1.62 Å Mutation No [2]
PDB Sequence
GETSVPPGSA
1443
LVGPSCVMDD
1453
FRDPQRWKEC
1463
AKQGKMPCYF
1473
DLIEENVYLT
1483

RMQCECTPLE
1513
IACGEDCLNR
1523
LLMIECSSRC
1533
PNGDYCSNRR
1543
FQRKQHADVE
1553

VILTEKKGWG
1563
LRAAKDLPSN
1573
TFVLEYCGEV
1583
LDHKEFKARV
1593
KEYARNKNIH
1603

YYFMALKNDE
1613
IIDATQKGNC
1623
SRFMNHSCEP
1633
NCETQKWTVN
1643
GQLRVGFFTT
1653

KLVPSGSELT
1663
FDYQFQRYGK
1673
EAQKCFCGSA
1683
NCRGYLGGEN
1693
RVSIRA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .76M or .76M2 or .76M3 or :376M;style chemicals stick;color identity;select .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1602 or .A:1603 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1669 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS1560
2.163
GLY1561
3.221
TRP1562
1.820
GLY1563
4.012
TYR1579
2.475
ILE1602
2.940
HIS1603
2.786
TYR1604
2.404
TYR1605
2.638
PHE1606
3.424
MET1607
3.290
SER1624
2.548
ARG1625
1.954
PHE1626
2.959
Residue
Distance (Å)
MET1627
1.881
ASN1628
2.328
HIS1629
2.113
SER1630
4.189
PHE1650
3.120
PHE1664
3.125
TYR1666
2.726
GLN1669
2.546
GLN1676
3.245
LYS1677
2.749
CYS1678
2.772
PHE1679
2.993
CYS1680
2.879
LEU1689
4.201
Ligand Name: [(2~{s},5~{r})-1-[(2~{r},3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-3,4-Bis(Oxidanyl)oxolan-2-Yl]-5-Azaniumyl-6-Oxidanyl-6-Oxidanylidene-Hexan-2-Yl]-(3-Oxidanylpropyl)azanium Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LSZ
Method X-ray diffraction Resolution 1.62 Å Mutation No [2]
PDB Sequence
GETSVPPGSA
1443
LVGPSCVMDD
1453
FRDPQRWKEC
1463
AKQGKMPCYF
1473
DLIEENVYLM
1497

QCECTPLIAC
1516
GEDCLNRLLM
1526
IECSSRCPNG
1536
DYCSNRRFQR
1546
KQHADVEVIL
1556

TEKKGWGLRA
1566
AKDLPSNTFV
1576
LEYCGEVLDH
1586
KEFKARVKEY
1596
ARNKNIHYYF
1606

MALKNDEIID
1616
ATQKGNCSRF
1626
MNHSCEPNCE
1636
TQKWTVNGQL
1646
RVGFFTTKLV
1656

PSGSELTFDY
1666
QFQRYGKEAQ
1676
KCFCGSANCR
1686
GYLGGENRVS
1696
IRA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .76K or .76K2 or .76K3 or :376K;style chemicals stick;color identity;select .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1602 or .A:1603 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1669 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS1560
2.175
GLY1561
3.227
TRP1562
1.788
GLY1563
3.998
TYR1579
2.647
ILE1602
2.939
HIS1603
2.745
TYR1604
2.398
TYR1605
2.642
PHE1606
2.991
MET1607
3.214
SER1624
3.892
ARG1625
1.966
PHE1626
2.981
Residue
Distance (Å)
MET1627
1.941
ASN1628
2.442
HIS1629
2.054
SER1630
4.128
PHE1650
4.313
PHE1664
3.030
TYR1666
2.848
GLN1669
2.607
GLN1676
3.318
LYS1677
2.698
CYS1678
2.741
PHE1679
3.024
CYS1680
2.887
LEU1689
4.199
Ligand Name: [(2~{s},5~{r})-1-[(2~{r},3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-3,4-Bis(Oxidanyl)oxolan-2-Yl]-5-Azaniumyl-6-Oxidanyl-6-Oxidanylidene-Hexan-2-Yl]-Propyl-Azanium Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LSS
Method X-ray diffraction Resolution 1.79 Å Mutation No [2]
PDB Sequence
LVGPSCVMDD
1453
FRDPQRWKEC
1463
AKQGKMPCYF
1473
DLIEENVYLT
1483
ERKMQCECTP
1503

LSKDERAQGE
1513
IACGEDCLNR
1523
LLMIECSSRC
1533
PNGDYCSNRR
1543
FQRKQHADVE
1553

VILTEKKGWG
1563
LRAAKDLPSN
1573
TFVLEYCGEV
1583
LDHKEFKARV
1593
KEYARNKNIH
1603

YYFMALKNDE
1613
IIDATQKGNC
1623
SRFMNHSCEP
1633
NCETQKWTVN
1643
GQLRVGFFTT
1653

KLVPSGSELT
1663
FDYQFQRYGK
1673
EAQKCFCGSA
1683
NCRGYLG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .76H or .76H2 or .76H3 or :376H;style chemicals stick;color identity;select .A:1559 or .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1602 or .A:1603 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1670 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS1559
4.878
LYS1560
2.174
GLY1561
3.081
TRP1562
1.903
GLY1563
4.130
TYR1579
2.512
ILE1602
3.218
HIS1603
2.648
TYR1604
2.275
TYR1605
2.658
PHE1606
3.306
MET1607
3.363
SER1624
3.710
ARG1625
1.955
PHE1626
2.953
Residue
Distance (Å)
MET1627
1.891
ASN1628
2.502
HIS1629
2.085
SER1630
4.152
PHE1650
4.268
PHE1664
3.005
TYR1666
2.855
ARG1670
4.166
GLN1676
2.906
LYS1677
2.809
CYS1678
2.775
PHE1679
2.914
CYS1680
2.861
LEU1689
3.367
Ligand Name: [(2~{s},5~{s})-1-[(2~{r},3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-3,4-Bis(Oxidanyl)oxolan-2-Yl]-5-Azaniumyl-6-Oxidanyl-6-Oxidanylidene-Hexan-2-Yl]-Pentyl-Azanium Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LT6
Method X-ray diffraction Resolution 2.05 Å Mutation No [2]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
MQCECTPLSK
1506

DERAQGEIAC
1516
GEDCLNRLLM
1526
IECSSRCPNG
1536
DYCSNRRFQR
1546
KQHADVEVIL
1556

TEKKGWGLRA
1566
AKDLPSNTFV
1576
LEYCGEVLDH
1586
KEFKARVKEY
1596
ARNKNIHYYF
1606

MALKNDEIID
1616
ATQKGNCSRF
1626
MNHSCEPNCE
1636
TQKWTVNGQL
1646
RVGFFTTKLV
1656

PSGSELTFDY
1666
QFQRYGKEAQ
1676
KCFCGSANCR
1686
GYLG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .76J or .76J2 or .76J3 or :376J;style chemicals stick;color identity;select .A:1559 or .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1603 or .A:1605 or .A:1617 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1669 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS1559
4.663
LYS1560
2.194
GLY1561
3.184
TRP1562
2.049
GLY1563
4.284
TYR1579
2.849
HIS1603
3.852
TYR1605
1.975
ALA1617
3.768
SER1624
2.664
ARG1625
1.885
PHE1626
3.129
MET1627
3.112
Residue
Distance (Å)
ASN1628
2.421
HIS1629
2.180
SER1630
4.253
PHE1650
3.689
PHE1664
2.827
TYR1666
2.417
GLN1669
3.060
GLN1676
3.183
LYS1677
2.775
CYS1678
2.823
PHE1679
2.780
CYS1680
2.942
LEU1689
3.429
Ligand Name: [(2~{r},5~{s})-1-[(2~{r},3~{s},4~{r},5~{r})-5-(6-Aminopurin-9-Yl)-3,4-Bis(Oxidanyl)oxolan-2-Yl]-5-Azaniumyl-6-Oxidanyl-6-Oxidanylidene-Hexan-2-Yl]-(Phenylmethyl)azanium Ligand Info
Structure Description Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives PDB:5LSX
Method X-ray diffraction Resolution 2.90 Å Mutation No [2]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTEM
1497
QCECTPLSKD
1507

ERAQGEIACG
1517
EDCLNRLLMI
1527
ECSSRCPNGD
1537
YCSNRRFQRK
1547
QHADVEVILT
1557

EKKGWGLRAA
1567
KDLPSNTFVL
1577
EYCGEVLDHK
1587
EFKARVKEYA
1597
RNKNIHYYFM
1607

ALKNDEIIDA
1617
TQKGNCSRFM
1627
NHSCEPNCET
1637
QKWTVNGQLR
1647
VGFFTTKLVP
1657

SGSELTFDYQ
1667
FQREAQKCFC
1680
GSANCRGYLG
1690
G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .76O or .76O2 or .76O3 or :376O;style chemicals stick;color identity;select .A:1557 or .A:1559 or .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1602 or .A:1603 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR1557
4.820
LYS1559
4.614
LYS1560
1.860
GLY1561
2.728
TRP1562
1.717
GLY1563
3.890
TYR1579
2.656
ILE1602
3.456
HIS1603
2.440
TYR1604
2.439
TYR1605
2.590
PHE1606
2.724
MET1607
3.505
SER1624
3.110
ARG1625
2.407
Residue
Distance (Å)
PHE1626
3.115
MET1627
2.681
ASN1628
2.442
HIS1629
2.376
SER1630
4.231
PHE1650
2.834
PHE1664
3.565
TYR1666
2.807
GLN1676
2.834
LYS1677
2.906
CYS1678
3.150
PHE1679
2.856
CYS1680
2.758
LEU1689
3.340
Ligand Name: N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-carboxamide Ligand Info
Structure Description Crystal Structure of SETD2 bound to Compound 35 PDB:7LZD
Method X-ray diffraction Resolution 1.80 Å Mutation No [1]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
RMQCECTPLS
1505

KDERAQGEIA
1515
CGEDCLNRLL
1525
MIECSSRCPN
1535
GDYCSNRRFQ
1545
RKQHADVEVI
1555

LTEKKGWGLR
1565
AAKDLPSNTF
1575
VLEYCGEVLD
1585
HKEFKARVKE
1595
YARNKNIHYY
1605

FMALKNDEII
1615
DATQKGNCSR
1625
FMNHSCEPNC
1635
ETQKWTVNGQ
1645
LRVGFFTTKL
1655

VPSGSELTFD
1665
YQFQRYGKEA
1675
QKCFCGSANC
1685
RGYLGGE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YHY or .YHY2 or .YHY3 or :3YHY;style chemicals stick;color identity;select .A:1579 or .A:1589 or .A:1593 or .A:1597 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1627 or .A:1628 or .A:1629 or .A:1664 or .A:1666 or .A:1668 or .A:1671 or .A:1672 or .A:1673 or .A:1674 or .A:1676 or .A:1689; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR1579
3.447
PHE1589
4.516
VAL1593
4.105
ALA1597
4.811
TYR1604
3.348
TYR1605
3.590
PHE1606
2.928
MET1607
4.013
MET1627
3.664
ASN1628
4.413
Residue
Distance (Å)
HIS1629
3.671
PHE1664
3.375
TYR1666
3.022
PHE1668
4.554
TYR1671
3.905
GLY1672
4.645
LYS1673
3.084
GLU1674
3.245
GLN1676
4.214
LEU1689
3.496
Ligand Name: (2s,5s)-2-Amino-6-[(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydrofuran-2-Yl]-5-(Propylamino)hexanoic Acid Ligand Info
Structure Description Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF PDB:4FMU
Method X-ray diffraction Resolution 2.10 Å Mutation No [3]
PDB Sequence
LVGPSCVMDD
1453
FRDPQRWKEC
1463
AKQGKMPCYF
1473
DLIEENVYLT
1483
MQCECTPLSK
1506

DERAQGEIAC
1516
GEDCLNRLLM
1526
IECSSRCPNG
1536
DYCSNRRFQR
1546
KQHADVEVIL
1556

TEKKGWGLRA
1566
AKDLPSNTFV
1576
LEYCGEVLDH
1586
KEFKARVKEY
1596
ARNKNIHYYF
1606

MALKNDEIID
1616
ATQKGNCSRF
1626
MNHSCEPNCE
1636
TQKWTVNGQL
1646
RVGFFTTKLV
1656

PSGSELTFDY
1666
QFQRYGKEAQ
1676
KCFCGSANCR
1686
GYLGG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0UM or .0UM2 or .0UM3 or :30UM;style chemicals stick;color identity;select .A:1559 or .A:1560 or .A:1561 or .A:1562 or .A:1563 or .A:1579 or .A:1602 or .A:1603 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1624 or .A:1625 or .A:1626 or .A:1627 or .A:1628 or .A:1629 or .A:1630 or .A:1650 or .A:1664 or .A:1666 or .A:1676 or .A:1677 or .A:1678 or .A:1679 or .A:1680 or .A:1689; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS1559
4.825
LYS1560
2.570
GLY1561
3.554
TRP1562
2.688
GLY1563
4.910
TYR1579
3.292
ILE1602
3.671
HIS1603
2.816
TYR1604
2.932
TYR1605
2.607
PHE1606
4.929
MET1607
4.114
SER1624
4.604
ARG1625
2.831
Residue
Distance (Å)
PHE1626
3.549
MET1627
3.275
ASN1628
2.813
HIS1629
2.913
SER1630
4.821
PHE1650
4.326
PHE1664
3.686
TYR1666
3.858
GLN1676
3.034
LYS1677
3.418
CYS1678
3.477
PHE1679
2.909
CYS1680
3.836
LEU1689
3.568
Ligand Name: N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide Ligand Info
Structure Description Crystal Structure of SETD2 bound to Compound 2 PDB:7LZB
Method X-ray diffraction Resolution 2.28 Å Mutation No [1]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
MQCECTPLSK
1506

DERAQGEIAC
1516
GEDCLNRLLM
1526
IECSSRCPNG
1536
DYCSNRRFQR
1546
KQHADVEVIL
1556

TEKKGWGLRA
1566
AKDLPSNTFV
1576
LEYCGEVLDH
1586
KEFKARVKEY
1596
ARNKNIHYYF
1606

MALKNDEIID
1616
ATQKGNCSRF
1626
MNHSCEPNCE
1636
TQKWTVNGQL
1646
RVGFFTTKLV
1656

PSGSELTFDY
1666
QFQRYGKEAQ
1676
KCFCGSANCR
1686
GYLGG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YJ1 or .YJ12 or .YJ13 or :3YJ1;style chemicals stick;color identity;select .A:1579 or .A:1589 or .A:1593 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1627 or .A:1628 or .A:1629 or .A:1664 or .A:1666 or .A:1668 or .A:1671 or .A:1672 or .A:1674 or .A:1676 or .A:1689; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR1579
3.405
PHE1589
4.970
VAL1593
3.918
TYR1604
3.259
TYR1605
3.624
PHE1606
2.956
MET1607
4.369
MET1627
3.557
ASN1628
4.301
Residue
Distance (Å)
HIS1629
3.813
PHE1664
3.560
TYR1666
3.047
PHE1668
4.004
TYR1671
3.297
GLY1672
4.940
GLU1674
3.368
GLN1676
4.357
LEU1689
4.176
Ligand Name: N-[(1R,3R)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide Ligand Info
Structure Description Crystal Structure of SETD2 Bound to an Indole-based Inhibitor PDB:7TY3
Method X-ray diffraction Resolution 2.30 Å Mutation No [4]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
RMQCECTPLS
1505

KDERAQGEIA
1515
CGEDCLNRLL
1525
MIECSSRCPN
1535
GDYCSNRRFQ
1545
RKQHADVEVI
1555

LTEKKGWGLR
1565
AAKDLPSNTF
1575
VLEYCGEVLD
1585
HKEFKARVKE
1595
YARNKNIHYY
1605

FMALKNDEII
1615
DATQKGNCSR
1625
FMNHSCEPNC
1635
ETQKWTVNGQ
1645
LRVGFFTTKL
1655

VPSGSELTFD
1665
YQFQRYGKEA
1675
QKCFCGSANC
1685
RGYLGGEN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KRF or .KRF2 or .KRF3 or :3KRF;style chemicals stick;color identity;select .A:1579 or .A:1597 or .A:1601 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1627 or .A:1628 or .A:1629 or .A:1664 or .A:1666 or .A:1668 or .A:1669 or .A:1670 or .A:1671 or .A:1674 or .A:1675 or .A:1676 or .A:1689; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR1579
3.558
ALA1597
4.883
ASN1601
4.225
TYR1604
3.158
TYR1605
3.372
PHE1606
2.837
MET1607
3.634
MET1627
3.776
ASN1628
4.410
HIS1629
3.589
Residue
Distance (Å)
PHE1664
3.436
TYR1666
2.809
PHE1668
3.457
GLN1669
3.991
ARG1670
3.935
TYR1671
3.486
GLU1674
3.653
ALA1675
4.792
GLN1676
3.921
LEU1689
3.656
Ligand Name: N-[(1R,3S)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide Ligand Info
Structure Description Crystal Structure of SETD2 Bound to an Indole-based Inhibitor PDB:7TY2
Method X-ray diffraction Resolution 2.44 Å Mutation No [4]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
MQCECTPLSK
1506

DERAEIACGE
1518
DCLNRLLMIE
1528
CSSRCPNGDY
1538
CSNRRFQRKQ
1548
HADVEVILTE
1558

KKGWGLRAAK
1568
DLPSNTFVLE
1578
YCGEVLDHKE
1588
FKARVKEYAR
1598
NKNIHYYFMA
1608

LKNDEIIDAT
1618
QKGNCSRFMN
1628
HSCEPNCETQ
1638
KWTVNGQLRV
1648
GFFTTKLVPS
1658

GSELTFDYQF
1668
QRYGKEAQKC
1678
FCGSANCRGY
1688
LGGE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KS6 or .KS62 or .KS63 or :3KS6;style chemicals stick;color identity;select .A:1579 or .A:1589 or .A:1593 or .A:1597 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1627 or .A:1628 or .A:1629 or .A:1664 or .A:1666 or .A:1668 or .A:1669 or .A:1671 or .A:1672 or .A:1673 or .A:1674 or .A:1676 or .A:1689; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR1579
3.526
PHE1589
3.879
VAL1593
4.008
ALA1597
4.222
TYR1604
3.324
TYR1605
3.469
PHE1606
2.960
MET1607
3.946
MET1627
3.558
ASN1628
4.395
HIS1629
3.451
Residue
Distance (Å)
PHE1664
3.458
TYR1666
3.011
PHE1668
3.578
GLN1669
4.825
TYR1671
3.167
GLY1672
4.571
LYS1673
4.980
GLU1674
3.344
GLN1676
4.385
LEU1689
3.561
Ligand Name: 4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl)(methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide Ligand Info
Structure Description Crystal Structure of SETD2 bound to Compound 57 PDB:7LZF
Method X-ray diffraction Resolution 2.47 Å Mutation No [1]
PDB Sequence
GPSCVMDDFR
1455
DPQRWKECAK
1465
QGKMPCYFDL
1475
IEENVYLTER
1485
KRMQCECTPL
1504

SKDERAQGEI
1514
ACGEDCLNRL
1524
LMIECSSRCP
1534
NGDYCSNRRF
1544
QRKQHADVEV
1554

ILTEKKGWGL
1564
RAAKDLPSNT
1574
FVLEYCGEVL
1584
DHKEFKARVK
1594
EYARNKNIHY
1604

YFMALKNDEI
1614
IDATQKGNCS
1624
RFMNHSCEPN
1634
CETQKWTVNG
1644
QLRVGFFTTK
1654

LVPSGSELTF
1664
DYQFQRYGKE
1674
AQKCFCGSAN
1684
CRGYLGGEN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .YHV or .YHV2 or .YHV3 or :3YHV;style chemicals stick;color identity;select .A:1579 or .A:1589 or .A:1593 or .A:1597 or .A:1604 or .A:1605 or .A:1606 or .A:1607 or .A:1627 or .A:1628 or .A:1629 or .A:1664 or .A:1666 or .A:1668 or .A:1669 or .A:1671 or .A:1672 or .A:1673 or .A:1674 or .A:1675 or .A:1676 or .A:1689; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR1579
3.441
PHE1589
4.244
VAL1593
4.236
ALA1597
3.771
TYR1604
3.129
TYR1605
3.661
PHE1606
2.912
MET1607
4.435
MET1627
3.504
ASN1628
4.254
HIS1629
3.539
Residue
Distance (Å)
PHE1664
3.485
TYR1666
2.975
PHE1668
3.812
GLN1669
4.848
TYR1671
3.332
GLY1672
3.487
LYS1673
3.399
GLU1674
3.176
ALA1675
4.938
GLN1676
4.197
LEU1689
3.609
References  Top
REF 1 Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies. ACS Med Chem Lett. 2021 Aug 24;12(10):1539-1545.
REF 2 Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives. ACS Chem Biol. 2016 Nov 18;11(11):3093-3105.
REF 3 Sinefungin derivatives as inhibitors and structure probes of protein lysine methyltransferase SETD2. J Am Chem Soc. 2012 Oct 31;134(43):18004-14.
REF 4 Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor for Clinical Studies. ACS Med Chem Lett. 2022 Jun 7;13(7):1137-1143.

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