SMTL ID : 9ggl.1

Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.177, H.179, D.265, G.302 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265, A:D.265

1 x 01: (1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl]cyclohexane-1,4-diamine

01.2: 14 residues within 4Å: Chain A: H.142, F.151, H.179, F.206, L.272, Y.304 Chain C: I.294, P.295, D.317, R.318, L.319, K.338, T.339, L.340 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.294, C:I.294, C:P.295, C:L.319, C:L.319, C:L.340, A:F.206 pi-Stacking: A:F.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Structural mimicry of UM171 and neomorphic cancer mutants co-opts E3 ligase KBTBD4 for HDAC1/2 recruitment. Nat Commun (2025)

Release Date

2025-04-09

Peptides

Histone deacetylase 2: A
Isoform 1 of Kelch repeat and BTB domain-containing protein 4: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Histone deacetylase 2

Isoform 1 of Kelch repeat and BTB domain-containing protein 4

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