SMTL ID : 9dtx.1

Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide

01.1: 28 residues within 4Å: Chain C: N.15, R.17, F.24, W.36, F.39, Y.46, P.47, R.55, I.57, H.58, S.59, Y.60, H.63, W.65 Chain D: V.53, F.54, L.57, P.58, E.62, L.63, Y.66, V.74, D.75, L.101, A.105, F.108, N.109, I.115 20 PLIP interactions: 11 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:R.17, C:F.39, C:I.57, C:W.65, D:D.75, D:L.101 Hydrogen bonds: C:R.55, C:H.58, C:S.59, C:Y.60, C:H.63, D:N.109, D:N.109 pi-Stacking: C:Y.46, C:Y.60, D:F.54 Water bridges: D:E.62, D:E.62 Salt bridges: D:E.62, D:E.62

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain B: E.76 Chain C: R.30, R.109, Q.112, V.113 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.30, C:R.109, C:R.109, C:Q.112, C:S.116

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 1 residues within 4Å: Chain C: P.47 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Y.46, C:Y.46

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

CL.4: 1 residues within 4Å: Chain C: P.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hulse, M. et al., PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers. Cancer Res. (2025)

Release Date

2025-10-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Transcription activator BRG1

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