9V36: Human DNMT1

Human DNMT1 (aa 698-1616) bound to hemimethylated dsDNA and Inhibitor DMI26. Determined by electron microscopy at 2.77 Å resolution. Released 18 Mar 2026.

Method

Electron microscopy

Resolution

2.77 Å

Organism

Homo sapiens

Chains

3

Atoms

7,054

Mol. weight

112.24 kDa

Ligands

A1EQT, SAH, ZN

Released

18 Mar 2026

Explore 9V36 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V36 contains 45 α-helices and 60 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.

Chain A: 45 helices, 60 β-strands

Molecules and chains

>9V36_1 DNA (cytosine-5)-methyltransferase 1 (chains A)
EADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETL
EVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLV
DECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFE
SPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGD
GVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIK
EIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQ
GRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGK
GKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAF
RLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNS
RTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFG
VLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRL
SSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDM
SALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCS
CVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQG
RVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCML
AKARESASAKIKEEEAAKD

>9V36_2 DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') (chains B)
ACTTACGGAAGG

>9V36_3 DNA (5'-D(*CP*CP*TP*TP*CP*CP*GP*TP*AP*AP*GP*T)-3') (chains E)
CCTTCCGTAAGT

Ligands and cofactors

Primary citation

Structure-guided design of 7-azaindole DNMT1 inhibitors active against hypomethylating agent-resistant acute myeloid leukemia. Tang, S., Zong, L., Ma, S. et al. Proc Natl Acad Sci U S A (2026) 123:e2532472123-e2532472123. DOI 10.1073/pnas.2532472123 · PubMed

Related structures

Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 6X9J 1.79 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052
• 6L1F 1.9 Å, Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1
• 7SFC 1.97 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A
• 5WVO 2.0 Å, Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated…
• 5YDR 2.0 Å, Structure of DNMT1 RFTS domain in complex with ubiquitin
• 7SFF 2.05 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B
• 7SFD 2.09 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A
• 6X9I 2.2 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA
• 7XIB 2.23 Å, Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and…
• 6K3A 2.3 Å, Crystal structure of human PCNA in complex with DNMT1 PIP box motif.
• 3EPZ 2.31 Å, Structure of the replication foci-targeting sequence of human DNA cytosine…
• 7SFG 2.43 Å, Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM

Browse structure collections

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