SMTL ID : 9hyn.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: (2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imidazo[1,2-a]quinazolin-2-yl)methyl]piperazin-1-yl]ethoxy]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

01.1: 34 residues within 4Å: Chain C: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: V.38, F.39, I.40, Q.41, L.42, P.43, L.48, Y.51, V.59, D.60, L.86, N.89, A.90, F.93, N.94, L.95, Q.99, I.100 25 PLIP interactions: 17 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:W.37, C:W.37, C:F.40, C:I.58, C:I.58, C:Y.61, C:W.66, D:L.42, D:D.60, D:F.93 Hydrogen bonds: C:Y.47, C:R.56, C:H.59, C:S.60, C:Y.61, C:Y.61, C:H.64, D:Y.51, D:N.94 Water bridges: C:H.59, C:H.64 pi-Stacking: C:Y.47, D:Y.51 Halogen bonds: D:L.86, D:N.94

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

2025-10-22

Peptides

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

Isoform Short of Probable global transcription activator SNF2L2

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