SMTL ID : 6w7g.1

Structure of EED bound to inhibitor 1056

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

3 x Q3A: 8-(2,6-dimethylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine(Non-covalent)

Q3A.1: 11 residues within 4Å: Chain A: F.24, N.73, Y.75, N.121, K.138, L.167, D.237, Y.292, M.293, R.294, R.341 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.24, A:F.24, A:Y.292, A:R.294 Hydrogen bonds: A:N.121, A:K.138 Water bridges: A:N.121 pi-Stacking: A:F.24, A:Y.75, A:Y.75, A:Y.292, A:Y.292, A:Y.292 pi-Cation interactions: A:R.294 Q3A.2: 14 residues within 4Å: Chain A: H.126, R.128, D.129, L.132, L.174, G.175, E.176, I.192, N.193, M.198, N.199, I.201, K.202, Y.205 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.128, A:I.201, A:K.202 Hydrogen bonds: A:D.129 Q3A.3: 8 residues within 4Å: Chain A: D.139, A.141, I.155, G.157, G.158, V.159, K.220, H.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.159 Water bridges: A:R.143

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: C.109, K.111, H.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.100, A:H.112

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 2 residues within 4Å: Chain A: K.111, I.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.111 Water bridges: A:S.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rej, R.K. et al., EEDi-5285: An Exceptionally Potent, Efficacious, and Orally Active Small-Molecule Inhibitor of Embryonic Ectoderm Development. J.Med.Chem. (2020)

Release Date

2020-07-08

Peptides

Polycomb protein EED: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polycomb protein EED

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