Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T88304 | Target Info | |||
| Target Name | DNA [cytosine-5]-methyltransferase 1 (DNMT1) | ||||
| Synonyms | MCMT; M.HsaI; Dnmt1; DNMT; DNA methyltransferase HsaI; DNA MTase HsaI; DNA (cytosine5)methyltransferase 1; DNA (cytosine-5)-methyltransferase 1; CXXCtype zinc finger protein 9; CXXC9; CXXC-type zinc finger protein 9; AIM | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | DNMT1 | ||||
| Biochemical Class | Methyltransferase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Ademetionine | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM | PDB:7SFG | ||||
| Method | X-ray diffraction | Resolution | 2.43 Å | Mutation | No | [1] |
| PDB Sequence |
RISWVGEAVK
739 TDGKKSYYKK749 VCIDAETLEV759 GDCVSVIPDD769 SSKPLYLARV779 TALWEDSSNG 789 QMFHAHWFCA799 GTDTVLGATS809 DPLELFLVDE819 CEDMQLSYIH829 SKVKVIYKAP 839 SENWAMEGGM849 DKTYFYQLWY869 DQDYARFESP879 PKTQPNKFKF892 CVSCARLAEM 902 RQKEIPRVLE912 QLEDLDSRVL922 YYSATKNGIL932 YRVGDGVYLP942 PEAFTFNIKP 963 VDEDLYPEHY973 RKYSDYIKGS983 NLDAPEPYRI993 GRIKEIFCPK1003 KSNGRPNETD 1013 IKIRVNKFYR1023 PENTHKSTPA1033 SYHADINLLY1043 WSDEEAVVDF1053 KAVQGRCTVE 1063 YGEDLPECVQ1073 VYSMGGPNRF1083 YFLEAYNAKS1093 KSFEDPPNHA1103 RKLPKLRTLD 1143 VFSGCGGLSE1153 GFHQAGISDT1163 LWAIEMWDPA1173 AQAFRLNNPG1183 STVFTEDCNI 1193 LLKLVMAGET1203 TNSRGQRLPQ1213 KGDVEMLCGG1223 PPCQGFSGMN1233 RFNSRTYSKF 1243 KNSLVVSFLS1253 YCDYYRPRFF1263 LLENVRNFVS1273 FKRSMVLKLT1283 LRCLVRMGYQ 1293 CTFGVLQAGQ1303 YGVAQTRRRA1313 IILAAAPGEK1323 LPLFPEPLHV1333 FAPRACQLSV 1343 VVDDKKFVSN1353 ITRLSSGPFR1363 TITVRDTMSD1373 LPEVRNGASA1383 LEISYNGEPQ 1393 SWFQRQLRGA1403 QYQPILRDHI1413 CKDMSALVAA1423 RMRHIPLAPG1433 SDWRDLPNIE 1443 VRLSDGTMAR1453 KLRYTHHDRK1463 NGRSSSGALR1473 GVCSCVEAGK1483 ACDPAARQFN 1493 TLIPWCLPHT1503 GNRHNHWAGL1513 YGRLEWDGFF1523 STTVTNPEPM1533 GKQGRVLHPE 1543 QHRVVSVREC1553 ARSQGFPDTY1563 RLFGNILDKH1573 RQVGNAVPPP1583 LAKAIGLEIK 1593 LCMLAKA
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PHE1145
3.160
SER1146
3.056
GLY1147
3.560
CYS1148
3.791
GLY1149
3.410
GLY1150
3.107
LEU1151
3.034
ILE1167
4.102
GLU1168
2.590
MET1169
3.333
TRP1170
3.144
ALA1173
4.504
|
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| Ligand Name: Sinefungin | Ligand Info | |||||
| Structure Description | Structure of human DNMT1 (601-1600) in complex with Sinefungin | PDB:3SWR | ||||
| Method | X-ray diffraction | Resolution | 2.49 Å | Mutation | No | [2] |
| PDB Sequence |
RQTIRHSTRE
610 PTKATTTKLV624 YQIFDTFFAE634 QINAFKRRRC653 GVCEVCQQPE663 CGKCKACKDM 673 VKFGGSGRSK683 QACQERRCPN693 MAMKEADDDE703 EVDDNIPEMP713 SPKKMHQGKK 723 KKQNKNRISW733 VGEAVKTDGK743 KSYYKKVCID753 AETLEVGDCV763 SVIPDDSSKP 773 LYLARVTALW783 EDSSNGQMFH793 AHWFCAGTDT803 VLGATSDPLE813 LFLVDECEDM 823 QLSYIHSKVK833 VIYKAPSENW843 AMEGGMDPES853 LLEGDDGKTY863 FYQLWYDQDY 873 ARFESPPKTQ883 PTEDNKFKFC893 VSCARLAEMR903 QKEIPRVLEQ913 LEDLDSRVLY 923 YSATKNGILY933 RVGDGVYLPP943 EAFTFNIKLS953 SPVKRPRKEP963 VDEDLYPEHY 973 RKYSDYIKGS983 NLDAPEPYRI993 GRIKEIFCPK1003 KSNGRPNETD1013 IKIRVNKFYR 1023 PENTHKSTPA1033 SYHADINLLY1043 WSDEEAVVDF1053 KAVQGRCTVE1063 YGEDLPECVQ 1073 VYSMGGPNRF1083 YFLEAYNAKS1093 KSFEDPPNHA1103 RSPEPEIEIK1135 LPKLRTLDVF 1145 SGCGGLSEGF1155 HQAGISDTLW1165 AIEMWDPAAQ1175 AFRLNNPGST1185 VFTEDCNILL 1195 KLVMAGETTN1205 SRGQRLPQKG1215 DVEMLCGGPP1225 CQGFSGMNRF1235 NSRTYSKFKN 1245 SLVVSFLSYC1255 DYYRPRFFLL1265 ENVRNFVSFK1275 RSMVLKLTLR1285 CLVRMGYQCT 1295 FGVLQAGQYG1305 VAQTRRRAII1315 LAAAPGEKLP1325 LFPEPLHVFA1335 PRACQLSVVV 1345 DDKKFVSNIT1355 RLSSGPFRTI1365 TVRDTMSDLP1375 EVRNGASALE1385 ISYNGEPQSW 1395 FQRQLRGAQY1405 QPILRDHICK1415 DMSALVAARM1425 RHIPLAPGSD1435 WRDLPNIEVR 1445 LSDGTMARKL1455 RYTHHDRKNG1465 RSSSGALRGV1475 CSCVEAGKAC1485 DPAARQFNTL 1495 IPWCLPHTGN1505 RHNHWAGLYG1515 RLEWDGFFST1525 TVTNPEPMGK1535 QGRVLHPEQH 1545 RVVSVRECAR1555 SQGFPDTYRL1565 FGNILDKHRQ1575 VGNAVPPPLA1585 KAIGLEIKLC 1595 MLAKA
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PHE1145
3.407
SER1146
3.138
GLY1147
3.412
CYS1148
3.754
GLY1149
3.468
GLY1150
3.363
LEU1151
2.870
ILE1167
4.020
GLU1168
2.693
MET1169
3.212
TRP1170
3.280
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| Ligand Name: Beta-D-Glucose | Ligand Info | |||||
| Structure Description | Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 | PDB:3EPZ | ||||
| Method | X-ray diffraction | Resolution | 2.31 Å | Mutation | No | [3] |
| PDB Sequence |
GPKCIQCGQY
359 LDDPDLKYGQ369 HPPDAVDEPQ379 LTNEKLSIFD390 ALPQHKLTCF410 SVYCKHGHLC 420 PIDTGLIEKN430 IELFFSGSAK440 PIPGGVNGKN457 LGPINEWWIT467 GGEKALIGFS 480 TSFAEYILDP491 SPEYAPIFGL501 QEKIYISKIV512 VEFLQSNSDS522 TYEDLINKIE 532 TTVPPSGLNL542 NRFTEDSLLR552 HAQFVVEQVE562 SYDEAGDQPI575 FLTPCRDLIK 586 LAGVTLGQRR596 AQA
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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 .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .A:404 or .A:463 or .A:465 or .A:466 or .A:467 or .A:480 or .A:485 or .A:514 or .A:517 or .A:564; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-(beta-D-Ribofuranosyl)-pyrimidin-2-one-5'-phosphate | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 | PDB:6X9J | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [4] |
| PDB Sequence |
NRISWVGEAV
738 KTDGKKSYYK748 KVCIDAETLE758 VGDCVSVIPD768 DSSKPLYLAR778 VTALWEDSSN 788 GQMFHAHWFC798 AGTDTVLGAT808 SDPLELFLVD818 ECEDMQLSYI828 HSKVKVIYKA 838 PSENWAMEGG848 MDPESLLEGD858 DGKTYFYQLW868 YDQDYARFES878 PPKTQPTEDN 888 KFKFCVSCAR898 LAEMRQKEIP908 RVLEQLEDLD918 SRVLYYSATK928 NGILYRVGDG 938 VYLPPEAFTF948 NIKLSSPVKR958 PRKEPVDEDL968 YPEHYRKYSD978 YIKGSNLDAP 988 EPYRIGRIKE998 IFCPKKSNGR1008 PNETDIKIRV1018 NKFYRPENTH1028 KSTPASYHAD 1038 INLLYWSDEE1048 AVVDFKAVQG1058 RCTVEYGEDL1068 PECVQVYSMG1078 GPNRFYFLEA 1088 YNAKSKSFED1098 PPNHARKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .PYO or .PYO2 or .PYO3 or :3PYO;style chemicals stick;color identity;select .A:1268 or .A:1269 or .A:1270 or .A:1271 or .A:1535; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Deoxy-5-methylcytidylic acid | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 | PDB:6X9J | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [4] |
| PDB Sequence |
NRISWVGEAV
738 KTDGKKSYYK748 KVCIDAETLE758 VGDCVSVIPD768 DSSKPLYLAR778 VTALWEDSSN 788 GQMFHAHWFC798 AGTDTVLGAT808 SDPLELFLVD818 ECEDMQLSYI828 HSKVKVIYKA 838 PSENWAMEGG848 MDPESLLEGD858 DGKTYFYQLW868 YDQDYARFES878 PPKTQPTEDN 888 KFKFCVSCAR898 LAEMRQKEIP908 RVLEQLEDLD918 SRVLYYSATK928 NGILYRVGDG 938 VYLPPEAFTF948 NIKLSSPVKR958 PRKEPVDEDL968 YPEHYRKYSD978 YIKGSNLDAP 988 EPYRIGRIKE998 IFCPKKSNGR1008 PNETDIKIRV1018 NKFYRPENTH1028 KSTPASYHAD 1038 INLLYWSDEE1048 AVVDFKAVQG1058 RCTVEYGEDL1068 PECVQVYSMG1078 GPNRFYFLEA 1088 YNAKSKSFED1098 PPNHARKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .5CM or .5CM2 or .5CM3 or :35CM;style chemicals stick;color identity;select .A:1498 or .A:1499 or .A:1500 or .A:1502 or .A:1503 or .A:1506 or .A:1507 or .A:1510 or .A:1513 or .A:1533 or .A:1534 or .A:1535; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 | PDB:6X9J | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [4] |
| PDB Sequence |
NRISWVGEAV
738 KTDGKKSYYK748 KVCIDAETLE758 VGDCVSVIPD768 DSSKPLYLAR778 VTALWEDSSN 788 GQMFHAHWFC798 AGTDTVLGAT808 SDPLELFLVD818 ECEDMQLSYI828 HSKVKVIYKA 838 PSENWAMEGG848 MDPESLLEGD858 DGKTYFYQLW868 YDQDYARFES878 PPKTQPTEDN 888 KFKFCVSCAR898 LAEMRQKEIP908 RVLEQLEDLD918 SRVLYYSATK928 NGILYRVGDG 938 VYLPPEAFTF948 NIKLSSPVKR958 PRKEPVDEDL968 YPEHYRKYSD978 YIKGSNLDAP 988 EPYRIGRIKE998 IFCPKKSNGR1008 PNETDIKIRV1018 NKFYRPENTH1028 KSTPASYHAD 1038 INLLYWSDEE1048 AVVDFKAVQG1058 RCTVEYGEDL1068 PECVQVYSMG1078 GPNRFYFLEA 1088 YNAKSKSFED1098 PPNHARKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .X52 or .X522 or .X523 or :3X52;style chemicals stick;color identity;select .A:1226 or .A:1227 or .A:1228 or .A:1230 or .A:1268 or .A:1274 or .A:1507 or .A:1510 or .A:1535; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl)phenyl]methyl}glycinamide | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A | PDB:7SFC | ||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | No | [1] |
| PDB Sequence |
RISWVGEAVK
739 TDGKKSYYKK749 VCIDAETLEV759 GDCVSVIPDD769 SSKPLYLARV779 TALWEDSSNG 789 QMFHAHWFCA799 GTDTVLGATS809 DPLELFLVDE819 CEDMQLSYIH829 SKVKVIYKAP 839 SENWAMEGGM849 DPESLLEGDD859 GKTYFYQLWY869 DQDYARFESP879 PKTQPTEDNK 889 FKFCVSCARL899 AEMRQKEIPR909 VLEQLEDLDS919 RVLYYSATKN929 GILYRVGDGV 939 YLPPEAFTFN949 IKLSSPVKRP959 RKEPVDEDLY969 PEHYRKYSDY979 IKGSNLDAPE 989 PYRIGRIKEI999 FCPKKSNGRP1009 NETDIKIRVN1019 KFYRPENTHK1029 STPASYHADI 1039 NLLYWSDEEA1049 VVDFKAVQGR1059 CTVEYGEDLP1069 ECVQVYSMGG1079 PNRFYFLEAY 1089 NAKSKSFEDP1099 PNHARSKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .I67 or .I672 or .I673 or :3I67;style chemicals stick;color identity;select .A:775 or .A:796 or .A:797 or .A:798 or .A:802 or .A:803 or .A:807 or .A:808 or .A:809 or .A:810 or .A:811 or .A:817 or .A:819 or .A:821 or .A:855 or .A:856 or .A:857 or .A:858 or .A:869 or .A:871 or .A:1234 or .A:1235 or .A:1236 or .A:1237 or .A:1240 or .A:1278 or .A:1282 or .A:1285 or .A:1226 or .A:1227 or .A:1228 or .A:1229 or .A:1230 or .A:1231 or .A:1507 or .A:1510 or .A:1535; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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TYR775
3.259
TRP796
3.282
PHE797
3.299
CYS798
3.664
ASP802
3.128
THR803
4.569
ALA807
3.028
THR808
3.675
SER809
3.296
ASP810
4.090
PRO811
4.032
VAL817
3.498
GLU819
4.001
GLU821
2.821
LEU855
4.934
GLU856
3.090
GLY857
4.671
ASP858
2.777
TYR869
4.061
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| Ligand Name: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl)phenyl]acetamide | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B | PDB:7SFF | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [1] |
| PDB Sequence |
RISWVGEAVK
739 TDGKKSYYKK749 VCIDAETLEV759 GDCVSVIPDD769 SSKPLYLARV779 TALWEDSSNG 789 QMFHAHWFCA799 GTDTVLGATS809 DPLELFLVDE819 CEDMQLSYIH829 SKVKVIYKAP 839 SENWAMEGGM849 DPESLLEGDD859 GKTYFYQLWY869 DQDYARFESP879 PKTQPTEDNK 889 FKFCVSCARL899 AEMRQKEIPR909 VLEQLEDLDS919 RVLYYSATKN929 GILYRVGDGV 939 YLPPEAFTFN949 IKLSSPVKRP959 RKEPVDEDLY969 PEHYRKYSDY979 IKGSNLDAPE 989 PYRIGRIKEI999 FCPKKSNGRP1009 NETDIKIRVN1019 KFYRPENTHK1029 STPASYHADI 1039 NLLYWSDEEA1049 VVDFKAVQGR1059 CTVEYGEDLP1069 ECVQVYSMGG1079 PNRFYFLEAY 1089 NAKSKSFEDP1099 PNHARSKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .C79 or .C792 or .C793 or :3C79;style chemicals stick;color identity;select .A:1230 or .A:1507 or .A:1510 or .A:1535; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]amino}-2-phenylacetamide | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830334A | PDB:7SFE | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [1] |
| PDB Sequence |
RISWVGEAVK
739 TDGKKSYYKK749 VCIDAETLEV759 GDCVSVIPDD769 SSKPLYLARV779 TALWEDSSNG 789 QMFHAHWFCA799 GTDTVLGATS809 DPLELFLVDE819 CEDMQLSYIH829 SKVKVIYKAP 839 SENWAMEGGM849 DPESLLEGDD859 GKTYFYQLWY869 DQDYARFESP879 PKTQPTEDNK 889 FKFCVSCARL899 AEMRQKEIPR909 VLEQLEDLDS919 RVLYYSATKN929 GILYRVGDGV 939 YLPPEAFTFN949 IKLSSPVKRP959 RKEPVDEDLY969 PEHYRKYSDY979 IKGSNLDAPE 989 PYRIGRIKEI999 FCPKKSNGRP1009 NETDIKIRVN1019 KFYRPENTHK1029 STPASYHADI 1039 NLLYWSDEEA1049 VVDFKAVQGR1059 CTVEYGEDLP1069 ECVQVYSMGG1079 PNRFYFLEAY 1089 NAKSKSFEDP1099 PNHARSKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .96I or .96I2 or .96I3 or :396I;style chemicals stick;color identity;select .A:1507 or .A:1510 or .A:1535; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide | Ligand Info | |||||
| Structure Description | Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A | PDB:6X9K | ||||
| Method | X-ray diffraction | Resolution | 2.65 Å | Mutation | No | [4] |
| PDB Sequence |
RISWVGEAVK
739 TDGKKSYYKK749 VCIDAETLEV759 GDCVSVIPDD769 SSKPLYLARV779 TALWEDSSNG 789 QMFHAHWFCA799 GTDTVLGATS809 DPLELFLVDE819 CEDMQLSYIH829 SKVKVIYKAP 839 SENWAMEGGM849 DPESLLEGDD859 GKTYFYQLWY869 DQDYARFESP879 PKTQPTEDNK 889 FKFCVSCARL899 AEMRQKEIPR909 VLEQLEDLDS919 RVLYYSATKN929 GILYRVGDGV 939 YLPPEAFTFN949 IKLSSPVKRP959 RKEPVDEDLY969 PEHYRKYSDY979 IKGSNLDAPE 989 PYRIGRIKEI999 FCPKKSNGRP1009 NETDIKIRVN1019 KFYRPENTHK1029 STPASYHADI 1039 NLLYWSDEEA1049 VVDFKAVQGR1059 CTVEYGEDLP1069 ECVQVYSMGG1079 PNRFYFLEAY 1089 NAKSKSFEDP1099 PNHARSKLPK1138 LRTLDVFSGC1148 GGLSEGFHQA1158 GISDTLWAIE 1168 MWDPAAQAFR1178 LNNPGSTVFT1188 EDCNILLKLV1198 MAGETTNSRG1208 QRLPQKGDVE 1218 MLCGGPPCQG1228 FSGMNRFNSR1238 TYSKFKNSLV1248 VSFLSYCDYY1258 RPRFFLLENV 1268 RNFVSFKRSM1278 VLKLTLRCLV1288 RMGYQCTFGV1298 LQAGQYGVAQ1308 TRRRAIILAA 1318 APGEKLPLFP1328 EPLHVFAPRA1338 CQLSVVVDDK1348 KFVSNITRLS1358 SGPFRTITVR 1368 DTMSDLPEVR1378 NGASALEISY1388 NGEPQSWFQR1398 QLRGAQYQPI1408 LRDHICKDMS 1418 ALVAARMRHI1428 PLAPGSDWRD1438 LPNIEVRLSD1448 GTMARKLRYT1458 HHDRKNGRSS 1468 SGALRGVCSC1478 VEAGKACDPA1488 ARQFNTLIPW1498 CLPHTGNRHN1508 HWAGLYGRLE 1518 WDGFFSTTVT1528 NPEPMGKQGR1538 VLHPEQHRVV1548 SVRECARSQG1558 FPDTYRLFGN 1568 ILDKHRQVGN1578 AVPPPLAKAI1588 GLEIKLCMLA1598 KA
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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 .UXM or .UXM2 or .UXM3 or :3UXM;style chemicals stick;color identity;select .A:1230 or .A:1507 or .A:1510 or .A:1535; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Selenomethionine | Ligand Info | |||||
| Structure Description | Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 | PDB:3EPZ | ||||
| Method | X-ray diffraction | Resolution | 2.31 Å | Mutation | No | [3] |
| PDB Sequence |
GPKCIQCGQY
359 LDDPDLKYGQ369 HPPDAVDEPQ379 LTNEKLSIFD390 ALPQHKLTCF410 SVYCKHGHLC 420 PIDTGLIEKN430 IELFFSGSAK440 PIPGGVNGKN457 LGPINEWWIT467 GGEKALIGFS 480 TSFAEYILDP491 SPEYAPIFGL501 QEKIYISKIV512 VEFLQSNSDS522 TYEDLINKIE 532 TTVPPSGLNL542 NRFTEDSLLR552 HAQFVVEQVE562 SYDEAGDQPI575 FLTPCRDLIK 586 LAGVTLGQRR596 AQA
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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 .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:375 or .A:376 or .A:377 or .A:378 or .A:379 or .A:381 or .A:382 or .A:383 or .A:384 or .A:405 or .A:406 or .A:407 or .A:408 or .A:410 or .A:422 or .A:423 or .A:439 or .A:453 or .A:455 or .A:458 or .A:464 or .A:476 or .A:477 or .A:486 or .A:487 or .A:488 or .A:490 or .A:491 or .A:498 or .A:499 or .A:500 or .A:501 or .A:503 or .A:504 or .A:506 or .A:507 or .A:512 or .A:516 or .A:540 or .A:542 or .A:557 or .A:558 or .A:561 or .A:575 or .A:576 or .A:577 or .A:578 or .A:579 or .A:580 or .A:582 or .A:583 or .A:584 or .A:585 or .A:586; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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VAL375
4.090
ASP376
2.822
GLU377
3.229
PRO378
3.300
GLN379
1.334
LEU381
1.326
THR382
3.300
ASN383
3.652
GLU384
3.107
HIS405
4.205
LYS406
4.191
LEU407
2.736
THR408
3.454
PHE410
3.461
ILE422
4.211
ASP423
3.722
ALA439
3.831
VAL453
3.830
GLY455
4.785
LEU458
4.634
TRP464
3.830
LEU476
4.943
ILE477
4.290
TYR486
3.150
ILE487
3.561
LEU488
1.336
ASP490
1.327
PRO491
3.922
ILE498
3.903
PHE499
3.332
GLY500
3.326
LEU501
1.328
GLN503
1.331
GLU504
3.918
ILE506
3.663
TYR507
4.249
VAL512
4.447
LEU516
3.689
LEU540
3.837
LEU542
3.453
VAL557
4.996
VAL558
3.781
VAL561
3.774
ILE575
3.214
PHE576
3.291
LEU577
4.799
THR578
3.092
PRO579
3.243
CYS580
1.336
ARG582
1.337
ASP583
3.177
LEU584
3.182
ILE585
2.867
LYS586
4.848
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure. 2022 Jun 2;30(6):793-802.e5. | ||||
| REF 2 | Structure of human DNMT1 (residues 600-1600) in complex with Sinefungin | ||||
| REF 3 | The replication focus targeting sequence (RFTS) domain is a DNA-competitive inhibitor of Dnmt1. J Biol Chem. 2011 Apr 29;286(17):15344-51. | ||||
| REF 4 | Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer. 2021 Oct;2(10):1002-1017. Epub 2021 Sep 27. | ||||
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