SMTL ID : 8g1q.1

Co-crystal structure of Compound 1 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.73 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: E.38, Q.42 Ligands: YHB.2, PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.38, A:Q.42

1 x YHB: N-(2-{4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}pyridine-4-carbonyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide(Non-covalent)

YHB.2: 27 residues within 4Å: Chain A: V.39, F.40, Q.42, L.43, P.44, E.48, L.49, Y.52, V.60, A.91, F.94, N.95, I.101 Chain D: N.16, R.18, F.25, W.37, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Ligands: NA.1 20 PLIP interactions: 7 interactions with chain A, 13 interactions with chain D Hydrophobic interactions: A:L.43, A:L.43, A:P.44, A:P.44, D:F.25, D:W.37, D:W.37, D:Y.47, D:I.58, D:Y.61, D:W.66 Hydrogen bonds: A:N.95, A:N.95, D:W.37, D:Y.47, D:H.59, D:Y.61, D:H.64 pi-Stacking: A:F.40, D:Y.47

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain D: P.46, Y.47, P.48 Ligands: NA.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wurz, R.P. et al., Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Nat Commun (2023)

Release Date

2023-07-26

Peptides

Transcription activator BRG1: A
Elongin-B: B
Elongin-C: C
von Hippel-Lindau disease tumor suppressor: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
B

D
C

Transcription activator BRG1

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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