SMTL ID : 8x7h.2 (3 other biounits)

Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x YBI: ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-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]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide

YBI.1: 24 residues within 4Å: Chain A: Q.10, I.39, L.42, T.43, E.45, Y.46, L.49, T.51, E.115, L.118, S.131, F.132, Y.136, Y.151 Chain B: P.40, F.41, V.45, L.52, Y.55, Y.97, N.98, D.103, I.104, M.107 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.39, A:L.42, A:L.42, A:L.49, A:T.51, A:L.118, A:F.132, B:P.40, B:P.40, B:F.41, B:V.45, B:Y.97, B:I.104 Hydrogen bonds: A:Q.10, A:E.45, A:E.115, A:E.115, A:S.131, A:Y.136, B:Y.55, B:N.98 Salt bridges: A:E.45

4 x GOL: GLYCEROL

GOL.2: 5 residues within 4Å: Chain B: I.58, K.60, T.61, N.93, I.96 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.58, B:K.60, B:K.60, B:T.61, B:N.93, B:N.93 GOL.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.5: 3 residues within 4Å: Chain B: N.75, Y.77, W.78 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., Crystal structure of 162. To Be Published

Release Date

2025-03-26

Peptides

Glucose-induced degradation protein 4 homolog: A
Bromodomain-containing protein 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Glucose-induced degradation protein 4 homolog

Bromodomain-containing protein 4

Related Entries With Identical Sequence