SMTL ID : 8qjr.1 (1 other biounit)

BRG1 bromodomain in complex with VBC via compound 17

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.17 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain B: N.70, S.71, S.72, T.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.72, B:T.73 PO4.2: 4 residues within 4Å: Chain C: H.74, N.142, V.143, Q.144 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.142, C:N.142, C:N.142, C:V.143, C:Q.144 Salt bridges: C:H.74 PO4.3: 2 residues within 4Å: Chain C: R.125, R.126 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.126 PO4.4: 5 residues within 4Å: Chain C: L.50, P.51, T.54, G.55, R.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.55 Salt bridges: C:R.56 PO4.7: 5 residues within 4Å: Chain D: N.9, L.10, T.11, K.12, H.69 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.9, D:L.10, D:T.11, D:T.11, D:K.12 Water bridges: D:H.69 Salt bridges: D:H.69

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain C: R.69, G.76, E.83, D.146, R.149 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.146, C:R.149

1 x VLH: (2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]pyridin-2-yl]oxycyclobutyl]oxypiperidin-1-yl]ethoxy]-1,2-oxazol-5-yl]-3-methyl-butanoyl]-N-[(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

VLH.6: 27 residues within 4Å: Chain C: R.18, F.25, P.35, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: V.36, F.37, L.40, P.41, E.45, L.46, Y.49, V.57, D.58, A.88, F.91, N.92, I.98 20 PLIP interactions: 12 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:P.48, C:I.58, C:H.59, C:W.66, D:L.40, D:L.40, D:P.41, D:D.58 Hydrogen bonds: C:Y.47, C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64, D:Y.49, D:N.92, D:N.92 pi-Stacking: C:Y.47, C:Y.61, D:F.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berlin, M. et al., PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. J.Med.Chem. (2024)

Release Date

2024-01-17

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
G

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Transcription activator BRG1

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