5YLT: SET7/9

Crystal structure of SET7/9 in complex with a cyproheptadine derivative. Determined by X-ray diffraction at 1.69 Å resolution. Released 20 Jun 2018.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,217
Mol. weight: 30.04 kDa
Ligands: C7N, SFG
Released: 20 Jun 2018

Explore 5YLT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YLT contains 8 α-helices and 22 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	1
β-strand	128-132	5	1
β-strand	141-147	7	1
β-strand	153-160	8	1
β-strand	163-176	14	1
β-strand	179-184	6	1
α-helix	185	1
β-strand	190-191	2	1
α-helix	210-215	6
β-strand	216-220	5	2
β-strand	228-232	5	2
β-strand	236	1	3
β-strand	241-245	5	4
β-strand	248-250	3	5
α-helix	252-256	5
β-strand	259	1	6
α-helix	260-262	3
β-strand	267-268	2	5
β-strand	274-276	3	5
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	4
β-strand	303-310	8	4
β-strand	314-321	8	4
β-strand	325	1	3
α-helix	329	1
β-strand	330-331	2	2
β-strand	332-333	2	4
β-strand	344	1	6
α-helix	351-362	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD7	A	protein	263	Homo sapiens	Q8WTS6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YLT_1 Histone-lysine N-methyltransferase SETD7 (chains A)
GSSGSSGKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGE
MIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLI
SSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNH
VSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPG
KSGPEAPEWYQVELKAFQATQQK

Ligands and cofactors

ID	Name	Formula	Copies
C7N	2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,…	C21 H21 N O	1
SFG	Sinefungin	C15 H23 N7 O5	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine. Hirano, T., Fujiwara, T., Niwa, H. et al. ChemMedChem (2018) 13:1530-1540. DOI 10.1002/cmdc.201800233 · PubMed

Other PDB entries of the same protein (UniProt Q8WTS6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F69 1.3 Å, Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide
3M58 1.4 Å, SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy
3CBP 1.42 Å, Set7/9-ER-Sinefungin complex
3M55 1.55 Å, SET7/9 Y305F in complex with TAF10-K189me1 peptide and AdoHcy
5EG2 1.55 Å, SET7/9 N265A in complex with AdoHcy and TAF10 peptide
4J7F 1.59 Å, SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy
3M54 1.6 Å, SET7/9 Y305F in complex with TAF10 peptide and AdoHcy
4J8O 1.63 Å, SET7/9 in complex with TAF10K189A peptide and AdoHcy
3CBO 1.65 Å, SET7/9-ER-AdoHcy complex
3M56 1.65 Å, SET7/9 Y305F in complex with TAF10-K189me2 peptide and AdoHcy
3CBM 1.69 Å, SET7/9-ER-AdoMet complex
3OS5 1.69 Å, SET7/9-Dnmt1 K142me1 complex

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