SMTL ID : 8g46.1

Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.104, C.107, C.181, C.183 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.104, B:C.107, B:C.181, B:C.183

1 x YK3: tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate(Covalent)

YK3.2: 14 residues within 4Å: Chain B: C.62, L.63, Y.66, W.185 Chain C: W.43, P.44, V.49, L.54, L.56, N.102, H.106, E.107, V.108, M.111 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.43, C:W.43, C:W.43, C:P.44, C:V.49, C:L.56, C:V.108, C:V.108, B:Y.66, B:W.185 Hydrogen bonds: C:N.102, C:E.107 Salt bridges: C:H.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y.D. et al., Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders. Biorxiv (2023)

Release Date

2023-03-08

Peptides

DNA damage-binding protein 1: A
DDB1- and CUL4-associated factor 16: B
Bromodomain-containing protein 4: C
DET1- and DDB1-associated protein 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

DNA damage-binding protein 1

DDB1- and CUL4-associated factor 16

Bromodomain-containing protein 4

DET1- and DDB1-associated protein 1

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