SMTL ID : 6w7f.1

Structure of EED bound to inhibitor 5285

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x Q3D: 8-(6-cyclopropylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine(Non-covalent)

Q3D.1: 12 residues within 4Å: Chain A: P.22, F.24, Y.75, N.121, K.138, L.167, D.237, Y.292, M.293, R.294, R.341, D.357 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.22, A:F.24, A:F.24, A:F.24, A:Y.292, A:R.294 Hydrogen bonds: A:N.121, A:K.138 pi-Stacking: A:Y.75, A:Y.75, A:Y.292, A:Y.292, A:Y.292 pi-Cation interactions: A:R.294 Q3D.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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.128, A:I.201, A:I.201, A:K.202 Hydrogen bonds: A:D.129, A:D.129 Water bridges: A:E.176 pi-Cation interactions: A:H.126

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 14 residues within 4Å: Chain A: G.97, G.115, H.116, G.117, N.118, A.119, I.120, S.135, V.136, S.137, D.139, A.141, R.143, W.145 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.115, A:H.116, A:G.117, A:N.118, A:N.118, A:S.135, A:S.137, A:D.139, A:R.143

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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