Human DNMT1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor DMT207. Determined by electron microscopy at 2.85 Å resolution. Released 8 Apr 2026.
Explore 9V5P in 3D Show helices and sheets RCSB PDB PDBe
9V5P contains 42 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 | 740-741 | 2 | 2 |
| β-strand | 744-747 | 4 | 2 |
| β-strand | 749-751 | 3 | 1 |
| β-strand | 756-758 | 3 | 1 |
| β-strand | 762-765 | 4 | 3 |
| α-helix | 773-774 | 2 | |
| β-strand | 775-776 | 2 | 3 |
| β-strand | 779-785 | 7 | 2 |
| β-strand | 790-799 | 10 | 2 |
| α-helix | 806-808 | 3 | |
| β-strand | 813-824 | 12 | 2 |
| α-helix | 825-827 | 3 | |
| β-strand | 828-832 | 5 | 3 |
| β-strand | 834-836 | 3 | 2 |
| α-helix | 851-854 | 4 | |
| β-strand | 863-870 | 8 | 2 |
| β-strand | 875-877 | 3 | 2 |
| α-helix | 878-880 | 3 | |
| α-helix | 883-885 | 3 | |
| α-helix | 886-888 | 3 | |
| α-helix | 894-905 | 12 | |
| β-strand | 909-910 | 2 | 4 |
| β-strand | 913-916 | 4 | 5 |
| β-strand | 920-923 | 4 | 5 |
| β-strand | 925-928 | 4 | 4 |
| β-strand | 931-934 | 4 | 4 |
| β-strand | 938-941 | 4 | 5 |
| α-helix | 972-974 | 3 | |
| α-helix | 987-989 | 3 | |
| β-strand | 992-1002 | 11 | 5 |
| β-strand | 1003 | 1 | 6 |
| β-strand | 1009 | 1 | 6 |
| β-strand | 1015-1022 | 8 | 5 |
| α-helix | 1024-1026 | 3 | |
| α-helix | 1033-1036 | 4 | |
| β-strand | 1041-1052 | 12 | 5 |
| α-helix | 1053-1055 | 3 | |
| β-strand | 1059-1064 | 6 | 5 |
| α-helix | 1072-1076 | 5 | |
| β-strand | 1082-1090 | 9 | 5 |
| β-strand | 1095-1097 | 3 | 5 |
| α-helix | 1098-1100 | 3 | |
| α-helix | 1135-1138 | 4 | |
| β-strand | 1139-1144 | 6 | 7 |
| α-helix | 1150-1158 | 9 | |
| β-strand | 1161-1167 | 7 | 7 |
| α-helix | 1171-1180 | 10 | |
| β-strand | 1185-1187 | 3 | 7 |
| α-helix | 1191-1200 | 10 | |
| β-strand | 1219-1221 | 3 | 7 |
| α-helix | 1234-1235 | 2 | |
| α-helix | 1237-1243 | 7 | |
| α-helix | 1247-1258 | 12 | |
| β-strand | 1262-1268 | 7 | 7 |
| α-helix | 1269-1272 | 4 | |
| α-helix | 1278-1290 | 13 | |
| β-strand | 1293-1300 | 8 | 7 |
| α-helix | 1301-1304 | 4 | |
| β-strand | 1308 | 1 | 8 |
| β-strand | 1311-1318 | 8 | 7 |
| β-strand | 1320 | 1 | 9 |
| β-strand | 1322 | 1 | 9 |
| α-helix | 1323-1330 | 8 | |
| β-strand | 1332 | 1 | 10 |
| α-helix | 1336-1338 | 3 | |
| β-strand | 1343-1344 | 2 | 11 |
| β-strand | 1349-1350 | 2 | 11 |
| β-strand | 1362 | 1 | 10 |
| α-helix | 1363-1365 | 3 | |
| α-helix | 1367-1371 | 5 | |
| α-helix | 1375-1376 | 2 | |
| β-strand | 1385-1387 | 3 | 12 |
| α-helix | 1395-1401 | 7 | |
| β-strand | 1408-1410 | 3 | 12 |
| α-helix | 1419-1427 | 9 | |
| α-helix | 1436-1438 | 3 | |
| β-strand | 1444-1445 | 2 | 13 |
| β-strand | 1451-1452 | 2 | 13 |
| β-strand | 1453 | 1 | 14 |
| α-helix | 1454 | 1 | |
| β-strand | 1459 | 1 | 15 |
| β-strand | 1474 | 1 | 15 |
| α-helix | 1477-1479 | 3 | |
| α-helix | 1484-1486 | 3 | |
| β-strand | 1494 | 1 | 14 |
| α-helix | 1499-1502 | 4 | |
| α-helix | 1508-1510 | 3 | |
| β-strand | 1515-1516 | 2 | 16 |
| β-strand | 1523 | 1 | 8 |
| β-strand | 1538-1540 | 3 | 16 |
| β-strand | 1547 | 1 | 16 |
| α-helix | 1550-1557 | 8 | |
| α-helix | 1569-1578 | 10 | |
| α-helix | 1580-1581 | 2 | |
| α-helix | 1582-1609 | 28 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| DNA (cytosine-5)-methyltransferase 1 | A | protein | 919 | Homo sapiens | P26358 (AlphaFold model) |
| DNA (5'-d(*cp*cp*tp*tp*cp*cp*gp*tp*ap*ap*gp*t)-3') | E | DNA | 12 | Homo sapiens | |
| DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') | B | DNA | 12 | Homo sapiens |
>9V5P_1 DNA (cytosine-5)-methyltransferase 1 (chains A) EADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETL EVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLV DECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFE SPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGD GVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIK EIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQ GRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGK GKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAF RLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNS RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRL SSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDM SALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCS CVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQG RVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCML AKARESASAKIKEEEAAKD
>9V5P_2 DNA (5'-D(*CP*CP*TP*TP*CP*CP*GP*TP*AP*AP*GP*T)-3') (chains E) CCTTCCGTAAGT
>9V5P_3 DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') (chains B) ACTTACGGAAGG
| ID | Name | Formula | Copies |
|---|---|---|---|
| A1EQ2 | (2~{R})-2-[3,5-dicyano-1-[2-[2-(dimethylamino)ethyl-methyl-amino]-2-oxidanylide… | C27 H31 N7 O3 S | 1 |
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
| ZN | Zinc ion | Zn | 2 |
Discovery of a Novel DNMT1 Inhibitor with Improved Efficacy in Treating beta-Thalassemia. Shen, Y., Wei, J., Tang, S. et al. Adv Sci (Weinh) (2026) 13:e13469-e13469. DOI 10.1002/advs.202513469 · PubMed
Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 9V5P directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.