6YVJ: EED

EED in complex with a triazolopyrimidine. Determined by X-ray diffraction at 1.84 Å resolution. Released 12 May 2021.

Method: X-ray diffraction
Resolution: 1.84 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,206
Mol. weight: 85.49 kDa
Ligands: L9W, EJR
Released: 12 May 2021

Explore 6YVJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YVJ contains 6 α-helices and 58 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: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	83-89	7	1
α-helix	94-95	2
β-strand	96-101	6	2
α-helix	105-106	2
β-strand	111-117	7	2
β-strand	120-126	7	2
β-strand	132-139	8	2
β-strand	147-154	8	3
β-strand	161-167	7	3
β-strand	172-176	5	3
β-strand	181-186	6	3
β-strand	193-198	6	4
β-strand	205-210	6	4
β-strand	215-219	5	4
β-strand	224-229	6	4
β-strand	239-244	6	5
β-strand	250-255	6	5
β-strand	260-264	5	5
α-helix	268-279	12
α-helix	288-291	4
β-strand	292-294	3	4
β-strand	299-301	3	5
β-strand	311-315	5	6
β-strand	318-322	5	6
β-strand	327-333	7	6
β-strand	350-357	8	6
β-strand	368-370	3	7
β-strand	376-380	5	7
β-strand	386-390	5	7
β-strand	402-404	3	7
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-438	6	1

Chain B: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	83-89	7	8
α-helix	94-96	3
β-strand	98-101	4	9
β-strand	111-117	7	9
β-strand	120-126	7	9
β-strand	132-139	8	9
β-strand	147-154	8	10
β-strand	161-167	7	10
β-strand	172-176	5	10
β-strand	181-186	6	10
β-strand	193-198	6	11
β-strand	205-210	6	11
β-strand	215-219	5	11
β-strand	224-229	6	11
β-strand	239-244	6	12
β-strand	250-255	6	12
β-strand	260-264	5	12
α-helix	268-278	11
β-strand	292-294	3	11
β-strand	299-301	3	12
β-strand	311-315	5	13
β-strand	318-322	5	13
β-strand	327-333	7	13
β-strand	350-357	8	13
β-strand	368-370	3	14
β-strand	376-380	5	14
β-strand	386-390	5	14
β-strand	402-404	3	14
β-strand	413-418	6	8
β-strand	424-429	6	8
β-strand	433-438	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein EED	A, B	protein	366	Homo sapiens	O75530 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6YVJ_1 Polycomb protein EED (chains A, B)
KKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLL
QSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINE
LKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCG
MDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWL
GDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQK
MLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIW
RWDRLR

Ligands and cofactors

ID	Name	Formula	Copies
L9W	N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triaz…	C21 H19 N5 O3 S	1
EJR	N-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-8-(2-methylpyridin-3-yl)-…	C20 H17 F N6 O	1

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

Primary citation

Free energy perturbation in the design of EED ligands as inhibitors of polycomb repressive complex 2 (PRC2) methyltransferase. O' Donovan, D.H., Gregson, C., Packer, M.J. et al. Bioorg Med Chem Lett (2021) 39:127904-127904. DOI 10.1016/j.bmcl.2021.127904 · PubMed

Other PDB entries of the same protein (UniProt O75530 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U69 1.28 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-d…
5U8F 1.34 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-i…
5U8A 1.45 Å, Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl…
6SFB 1.52 Å, EED in complex with a triazolopyrimidine
3K26 1.58 Å, Complex structure of EED and trimethylated H3K4
5U5T 1.6 Å, Crystal structure of EED in complex with H3K27Me3 peptide and…
7QK4 1.6 Å, EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683)
7P3C 1.61 Å, EED in complex with compound 4
6V3Y 1.63 Å, Crystal structure of EED in complex with PALI1-K1219me3 peptide
5U6D 1.64 Å, Polycomb protein EED in complex with inhibitor: 2-[4-(4-{(3S,4R)-4-(dimethylamino)-1-[(2-…
6V3X 1.7 Å, Crystal structure of EED in complex with PALI1-K1241me3 peptide
5TTW 1.74 Å, Crystal Structure of EED in Complex with UNC4859

Browse structure collections

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