9CR7: Human SETD8

Structure of human SETD8 in complex with covalent inhibitor AM2928. Determined by X-ray diffraction at 2.05 Å resolution. Released 30 Jul 2025.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,399
Mol. weight: 41.34 kDa
Ligands: H81, E1J
Released: 30 Jul 2025

Explore 9CR7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CR7 contains 12 α-helices and 26 β-strands across 2 chains. 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: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	236-253	18
β-strand	259-264	6	1
β-strand	267-273	7	1
β-strand	277	1	2
β-strand	282-285	4	3
β-strand	289-291	3	4
α-helix	293-304	12
β-strand	313-317	5	4
β-strand	322-326	5	4
α-helix	335-337	3
α-helix	338	1
β-strand	339-340	2	3
β-strand	346-353	8	3
β-strand	356-363	8	3
β-strand	367	1	2
α-helix	371	1
β-strand	372	1	1
α-helix	373	1
β-strand	374-376	3	3

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	240-253	14
β-strand	259-264	6	5
β-strand	267-273	7	5
β-strand	277	1	6
β-strand	282-285	4	7
β-strand	289-292	4	8
α-helix	293-304	12
β-strand	313-317	5	8
β-strand	322-326	5	8
α-helix	335-337	3
α-helix	338	1
β-strand	339-340	2	7
β-strand	346-353	8	7
β-strand	356-363	8	7
β-strand	367	1	6
α-helix	371	1
β-strand	372	1	5
α-helix	373	1
β-strand	374-376	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-lysine methyltransferase KMT5A	A, B	protein	176	Homo sapiens	Q9NQR1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9CR7_1 N-lysine methyltransferase KMT5A (chains A, B)
MSYYHHHHHHDYDIPTTENLYFQGAMGSRKSKAELQSEERKRIDELIESGKEEGMKIDLI
DGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYC
VDATRETNRLGRLINHSKSGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDR

Ligands and cofactors

ID	Name	Formula	Copies
H81	N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}pro…	C21 H28 N6 O3	1
E1J	N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}pro…	C21 H30 N6 O3	1

Primary citation

Discovery of a Potent, Selective, and In Vivo Efficacious Covalent Inhibitor for Lysine Methyltransferase SETD8. Chen, H., Dutta, R.P., Li, Z. et al. J Med Chem (2026) 69:4255-4269. DOI 10.1021/acs.jmedchem.5c02958 · PubMed

Other PDB entries of the same protein (UniProt Q9NQR1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F9X 1.25 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
5TEG 1.3 Å, Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and…
1ZKK 1.45 Å, Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy
2BQZ 1.5 Å, Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7…
3F9Y 1.5 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
3F9W 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
3F9Z 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
5W1Y 1.7 Å, SETD8 in complex with a covalent inhibitor
5TH7 1.95 Å, Complex of SETD8 with MS453
4IJ8 2.0 Å, Crystal structure of the complex of SETD8 with SAM
5V2N 2.0 Å, Crystal Structure of APO Human SETD8
5T5G 2.1 Å, human SETD8 in complex with MS2177

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