SMTL ID : 9hyb.3 (3 other biounits)

CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide

01.1: 37 residues within 4Å: Chain C: N.16, R.18, F.25, P.35, W.37, F.40, Q.45, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: E.37, V.38, F.39, I.40, Q.41, L.42, P.43, S.44, E.47, L.48, Y.51, V.59, D.60, L.86, N.89, A.90, F.93, N.94, Q.99, I.100 22 PLIP interactions: 11 interactions with chain D, 11 interactions with chain C Hydrophobic interactions: D:V.38, D:Q.41, D:P.43, D:L.48, D:F.93, C:F.40, C:I.58, C:Y.61, C:W.66 Hydrogen bonds: D:Y.51, D:N.94, C:Y.47, C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64 Salt bridges: D:E.47 pi-Stacking: D:F.39, D:Y.51, C:Y.47 Halogen bonds: D:L.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, N. et al., Frustration in the protein-protein interface plays a central role in the cooperativity of PROTAC ternary complexes. Nat Commun (2025)

Release Date

2025-11-12

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
Probable global transcription activator SNF2L2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
O

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Probable global transcription activator SNF2L2

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