SMTL ID : 6hr2.2 (1 other biounit)

Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 4 residues within 4Å: Chain A: V.36, I.98 Chain B: H.50 Ligands: FWZ.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.50 Water bridges: A:I.98

1 x FWZ: (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

FWZ.2: 33 residues within 4Å: Chain A: V.36, F.37, Q.39, L.40, P.41, L.46, Y.49, V.57, D.58, L.84, N.87, A.88, F.91, N.92, L.93, I.98 Chain B: N.7, R.9, F.16, P.26, W.28, F.31, Y.38, P.39, L.41, R.47, I.49, H.50, S.51, Y.52, H.55, W.57 Ligands: DMS.1 26 PLIP interactions: 9 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:L.40, A:L.46, A:D.58, A:F.91, B:W.28, B:W.28, B:Y.38, B:P.39, B:I.49, B:Y.52, B:W.57 Hydrogen bonds: A:Y.49, A:N.92, A:N.92, B:Y.38, B:R.47, B:H.50, B:S.51, B:Y.52, B:Y.52, B:H.55 pi-Stacking: A:F.37, B:Y.38 Halogen bonds: A:N.92 Water bridges: B:H.50, B:H.55

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

EDO.3: 8 residues within 4Å: Chain B: L.69, P.94, V.95 Chain C: Y.68, T.69, N.70, S.71, I.75 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.70, B:V.95, B:V.95 Water bridges: C:S.71 EDO.4: 4 residues within 4Å: Chain D: Y.45, D.48, A.87, L.88 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farnaby, W. et al., BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat.Chem.Biol. (2019)

Release Date

2019-06-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Transcription activator BRG1

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

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