SMTL ID : 7kxt.1 (1 other biounit)

Crystal structure of human EED

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x XB7: 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine(Non-covalent)

XB7.1: 15 residues within 4Å: Chain A: L.207, L.276, G.277, L.279, C.291, M.297, L.314, F.317, F.333, W.334, Q.335, L.352, P.357, H.358 Ligands: UNX.19 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.276, A:L.279, A:L.314, A:W.334, A:W.334, A:Q.335, A:P.357

27 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 2 residues within 4Å: Chain A: I.251, Q.253 Ligand excluded by PLIP UNX.3: 2 residues within 4Å: Chain A: I.251, K.254 Ligand excluded by PLIP UNX.4: 4 residues within 4Å: Chain A: I.189, G.191, K.254, I.255 Ligand excluded by PLIP UNX.5: 2 residues within 4Å: Chain A: S.48, L.49 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: Y.109, W.325 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: M.331, Q.335 Ligands: UNX.25 Ligand excluded by PLIP UNX.8: 6 residues within 4Å: Chain A: G.131, Y.147, V.148, G.149, H.150, W.179 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: A.112, K.158, F.159 Ligands: UNX.10 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: Q.61, A.112, K.158 Ligands: UNX.9 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: R.248, P.249, I.251 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: N.310, V.311 Ligand excluded by PLIP UNX.13: 5 residues within 4Å: Chain A: R.263, D.264, H.266, R.267 Ligands: UNX.14 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: R.263, D.264 Ligands: UNX.13 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: T.364, L.365, T.366 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: H.266, E.286 Ligand excluded by PLIP UNX.17: 6 residues within 4Å: Chain A: Y.269, C.285, D.323, I.324, W.325 Ligands: UNX.27 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: V.311, T.312, I.313 Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain A: L.276, G.277, D.278 Ligands: XB7.1 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain A: L.314, G.315, H.358 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: N.268, E.286 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: R.316, F.317, D.318, H.358 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: Q.61, F.62, W.64 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain A: T.185, L.186 Ligand excluded by PLIP UNX.25: 6 residues within 4Å: Chain A: D.204, R.274, W.275, M.331, Q.335 Ligands: UNX.7 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain A: S.228, K.229 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain A: I.324, W.325 Ligands: UNX.17 Ligand excluded by PLIP UNX.28: 5 residues within 4Å: Chain A: R.225, D.259, I.304, K.305, P.306 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, D. et al., Structure-Guided Development of Small-Molecule PRC2 Inhibitors Targeting EZH2-EED Interaction. J.Med.Chem. (2021)

Release Date

2021-02-24

Peptides

Polycomb protein EED: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polycomb protein EED

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