5U69: Polycomb protein EED

Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine. Determined by X-ray diffraction at 1.28 Å resolution. Released 15 Mar 2017.

Method: X-ray diffraction
Resolution: 1.28 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,442
Mol. weight: 42.95 kDa
Ligands: LQD
Released: 15 Mar 2017

Explore 5U69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U69 contains 7 α-helices and 29 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: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	83-89	7	1
β-strand	96-101	6	2
α-helix	105-106	2
α-helix	110	1
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	171-175	5	3
β-strand	182-187	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	282-284	3
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
α-helix	340-342	3
β-strand	350-357	8	6
β-strand	368-370	3	7
β-strand	376-380	5	7
β-strand	386-390	5	7
α-helix	396-398	3
β-strand	400-404	5	7
β-strand	413-418	6	1
β-strand	424-429	6	1
β-strand	433-438	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polycomb protein EED	A	protein	369	Homo sapiens	O75530 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5U69_1 Polycomb protein EED (chains A)
GSHMKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEI
RLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNA
INELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIM
SCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCV
RWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDF
WQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDA
SIWRWDRLR

Ligands and cofactors

ID	Name	Formula	Copies
LQD	(3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolid…	C23 H29 N3 O	1

Primary citation

SAR of amino pyrrolidines as potent and novel protein-protein interaction inhibitors of the PRC2 complex through EED binding. Curtin, M.L., Pliushchev, M.A., Li, H.Q. et al. Bioorg Med Chem Lett (2017) 27:1576-1583. DOI 10.1016/j.bmcl.2017.02.030 · PubMed

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

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
7SI5 1.75 Å, Crystal structure of eed with mrtx-1919

Browse structure collections

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