SMTL ID : 8ov6.1

Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: C.102, H.104, C.105, C.179, C.181 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.102, B:C.105, B:C.179, B:C.181

1 x U79: methyl 2-[(9~{S})-7-[4-[4-[[4-[(3-cyano-4-methyl-1~{H}-indol-7-yl)sulfamoyl]phenyl]methylcarbamoyl]phenyl]phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate(Non-covalent)

U79.2: 35 residues within 4Å: Chain B: W.56, C.60, L.61, K.63, Y.64, C.180, W.183 Chain C: W.41, P.42, F.43, V.47, L.52, L.54, Y.57, N.95, C.96, Y.99, N.100, D.105, I.106, M.109, W.334, P.335, F.336, V.340, L.345, L.347, C.389, Y.392, N.393, H.397, E.398, V.399, A.401, M.402 16 PLIP interactions: 3 interactions with chain B, 13 interactions with chain C Hydrophobic interactions: B:Y.64, B:W.183, C:W.41, C:V.47, C:W.334, C:F.336, C:V.340, C:L.345, C:L.347, C:E.398, C:E.398 Hydrogen bonds: B:W.56, C:N.393, C:E.398, C:E.398 Salt bridges: C:H.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsia, O. et al., Targeted protein degradation via intramolecular bivalent glues. Nature (2024)

Release Date

2023-05-17

Peptides

DDB1deltaBPB: A
DDB1- and CUL4-associated factor 16: B
Bromodomain-containing protein 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DDB1deltaBPB

DDB1- and CUL4-associated factor 16

Bromodomain-containing protein 4

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