SMTL ID : 9ggn.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 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

01.1: 13 residues within 4Å: Chain A: I.294, P.295, R.296, L.319, T.339, L.340 Chain B: E.99, H.142, F.151, H.179, F.206, L.272, Y.304 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:E.99, B:F.151, B:F.206, B:F.206, A:I.294, A:I.294, A:P.295, A:L.319, A:L.319, A:L.340 pi-Stacking: B:F.151, B:F.206 Hydrogen bonds: A:R.296 01.3: 13 residues within 4Å: Chain C: I.294, P.295, R.296, L.319, T.339, L.340 Chain D: E.99, H.142, F.151, H.179, F.206, L.272, Y.304 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.294, C:I.294, C:P.295, C:L.319, C:L.319, C:L.340, D:E.99, D:F.151, D:F.206, D:F.206 Hydrogen bonds: C:R.296 pi-Stacking: D:F.151, D:F.206

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain B: D.177, H.179, D.265 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.177, B:D.177, B:H.179, B:D.265 ZN.4: 3 residues within 4Å: Chain D: D.177, H.179, D.265 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.177, D:D.177, D:H.179, D:D.265

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

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

Histone deacetylase 2

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