SMTL ID : 8ymb.2 (1 other biounit)

The crystal structure of SHD931 in complex with Brd4-BD2 and VCB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 1 residues within 4Å: Chain B: R.13 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain C: R.68, S.72, S.73, T.74 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain D: N.15, R.17 Ligand excluded by PLIP

1 x 01: SHD931

01.4: 26 residues within 4Å: Chain A: W.42, P.43, F.44, A.52, L.53, G.54, L.55, C.97, N.101, H.105, E.106, V.107, M.110 Chain D: R.17, P.34, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 27 PLIP interactions: 17 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:R.17, D:W.36, D:W.36, D:F.39, D:P.47, D:I.57, D:I.57, D:Y.60, D:Y.60, D:W.65, A:W.42, A:P.43, A:P.43, A:F.44, A:L.53, A:L.53, A:L.55, A:V.107 Hydrogen bonds: D:Y.46, D:R.55, D:H.58, D:S.59, D:Y.60, D:H.63, A:N.101, A:N.101 pi-Stacking: D:Y.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C. et al., Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs. Jacs Au (2024)

Release Date

2025-02-12

Peptides

Bromodomain-containing protein 4: A
Elongin-B: B
Elongin-C: C
von Hippel-Lindau disease tumor suppressor: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

Bromodomain-containing protein 4

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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