Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052. Determined by X-ray diffraction at 1.79 Å resolution. Released 7 Jul 2021.
Explore 6X9J in 3D Show helices and sheets RCSB PDB PDBe
6X9J contains 52 α-helices and 54 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 732-733 | 2 | 1 |
| β-strand | 739-741 | 3 | 2 |
| β-strand | 744-746 | 3 | 2 |
| β-strand | 749-752 | 4 | 1 |
| β-strand | 755-758 | 4 | 1 |
| β-strand | 762-765 | 4 | 2 |
| β-strand | 775-785 | 11 | 2 |
| β-strand | 789-799 | 11 | 2 |
| α-helix | 800-802 | 3 | |
| α-helix | 806-808 | 3 | |
| β-strand | 813-824 | 12 | 2 |
| α-helix | 825-827 | 3 | |
| β-strand | 828-832 | 5 | 2 |
| β-strand | 834-836 | 3 | 2 |
| α-helix | 838-840 | 3 | |
| α-helix | 843-845 | 3 | |
| α-helix | 851-856 | 6 | |
| β-strand | 863-870 | 8 | 2 |
| β-strand | 875-877 | 3 | 2 |
| α-helix | 878-880 | 3 | |
| α-helix | 894-906 | 13 | |
| β-strand | 909-916 | 8 | 3 |
| β-strand | 920-928 | 9 | 3 |
| β-strand | 931-934 | 4 | 3 |
| β-strand | 938-941 | 4 | 3 |
| α-helix | 943-945 | 3 | |
| α-helix | 972-975 | 4 | |
| α-helix | 987-991 | 5 | |
| β-strand | 992-1002 | 11 | 3 |
| β-strand | 1003 | 1 | 4 |
| α-helix | 1004 | 1 | |
| β-strand | 1009 | 1 | 4 |
| β-strand | 1015-1022 | 8 | 3 |
| α-helix | 1023 | 1 | |
| α-helix | 1024-1026 | 3 | |
| α-helix | 1031-1034 | 4 | |
| β-strand | 1041-1052 | 12 | 3 |
| α-helix | 1053-1055 | 3 | |
| β-strand | 1058-1064 | 7 | 3 |
| α-helix | 1065-1067 | 3 | |
| α-helix | 1072-1077 | 6 | |
| β-strand | 1082-1088 | 7 | 3 |
| β-strand | 1089-1090 | 2 | 5 |
| β-strand | 1095-1096 | 2 | 5 |
| α-helix | 1136-1138 | 3 | |
| β-strand | 1139-1144 | 6 | 2 |
| α-helix | 1150-1158 | 9 | |
| β-strand | 1161-1167 | 7 | 2 |
| α-helix | 1171-1180 | 10 | |
| β-strand | 1185-1187 | 3 | 2 |
| α-helix | 1191-1199 | 9 | |
| β-strand | 1204 | 1 | 6 |
| α-helix | 1209 | 1 | |
| β-strand | 1210 | 1 | 6 |
| α-helix | 1211-1212 | 2 | |
| β-strand | 1219-1222 | 4 | 2 |
| α-helix | 1234-1235 | 2 | |
| α-helix | 1237-1244 | 8 | |
| α-helix | 1247-1258 | 12 | |
| β-strand | 1262-1268 | 7 | 2 |
| α-helix | 1269-1272 | 4 | |
| α-helix | 1274-1290 | 17 | |
| β-strand | 1293-1300 | 8 | 2 |
| α-helix | 1301-1304 | 4 | |
| β-strand | 1308 | 1 | 7 |
| β-strand | 1311-1318 | 8 | 2 |
| α-helix | 1323-1330 | 8 | |
| β-strand | 1332 | 1 | 8 |
| α-helix | 1336-1338 | 3 | |
| β-strand | 1343-1345 | 3 | 9 |
| β-strand | 1348-1350 | 3 | 9 |
| β-strand | 1362 | 1 | 8 |
| α-helix | 1363-1365 | 3 | |
| α-helix | 1367-1371 | 5 | |
| α-helix | 1375-1376 | 2 | |
| β-strand | 1385-1386 | 2 | 10 |
| α-helix | 1395-1401 | 7 | |
| β-strand | 1409-1410 | 2 | 10 |
| α-helix | 1419-1426 | 8 | |
| α-helix | 1436-1438 | 3 | |
| β-strand | 1444-1445 | 2 | 11 |
| β-strand | 1451-1452 | 2 | 11 |
| β-strand | 1453 | 1 | 12 |
| α-helix | 1454-1455 | 2 | |
| β-strand | 1459 | 1 | 13 |
| β-strand | 1466 | 1 | 14 |
| β-strand | 1472 | 1 | 14 |
| β-strand | 1474 | 1 | 13 |
| α-helix | 1477-1480 | 4 | |
| α-helix | 1487-1489 | 3 | |
| β-strand | 1494 | 1 | 12 |
| α-helix | 1499-1503 | 5 | |
| α-helix | 1504-1506 | 3 | |
| α-helix | 1508-1510 | 3 | |
| α-helix | 1515 | 1 | |
| β-strand | 1516 | 1 | 15 |
| α-helix | 1517 | 1 | |
| β-strand | 1523 | 1 | 7 |
| α-helix | 1524-1526 | 3 | |
| β-strand | 1540 | 1 | 15 |
| β-strand | 1547 | 1 | 15 |
| α-helix | 1548-1549 | 2 | |
| α-helix | 1550-1556 | 7 | |
| α-helix | 1569-1577 | 9 | |
| α-helix | 1580-1581 | 2 | |
| α-helix | 1582-1598 | 17 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| DNA (cytosine-5)-methyltransferase 1 | A | protein | 874 | Homo sapiens | P26358 (AlphaFold model) |
| DNA (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3') | C | DNA | 12 | Homo sapiens | |
| DNA (5'-d(*gp*cp*ap*gp*g)-r(p*(pyo))-d(p*gp*gp*cp*cp*tp*c)-3') | D | DNA | 12 | Homo sapiens |
>6X9J_1 DNA (cytosine-5)-methyltransferase 1 (chains A) HMNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDS SNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAME GGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKE IPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDE DLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPEN THKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFL EAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFS GCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNS RGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLE NVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPL FPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEI SYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRL SDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNR HNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLF GNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA
>6X9J_2 DNA (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3') (chains C) GAGGCCGCCTGC
>6X9J_3 DNA (5'-D(*GP*CP*AP*GP*G)-R(P*(PYO))-D(P*GP*GP*CP*CP*TP*C)-3') (chains D) GCAGGUGGCCTC
| ID | Name | Formula | Copies |
|---|---|---|---|
| X52 | N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)s… | C22 H28 N6 O2 S2 | 1 |
| ZN | Zinc ion | Zn | 2 |
Water and common crystallization additives (EDO) are not listed.
Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Pappalardi, M.B., Keenan, K., Cockerill, M. et al. Nat Cancer (2021) 2:1002-1017. PubMed
Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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