SMTL ID : 9hyo.1

CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.74 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[7-(5-bromanyl-4-oxidanylidene-2,3-dihydro-1,3-benzoxazin-2-yl)-4-[cyclopropyl(methyl)amino]-5,6,8,9-tetrahydropyrimido[4,5-d]azepin-2-yl]piperazin-1-yl]ethoxy]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: 31 residues within 4Å: Chain A: V.38, F.39, Q.41, L.42, P.43, L.48, E.50, Y.51, V.59, L.86, N.89, A.90, F.93, N.94, I.100 Chain D: N.16, R.18, F.25, P.35, W.37, F.40, P.46, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 20 PLIP interactions: 7 interactions with chain A, 13 interactions with chain D Hydrophobic interactions: A:L.42, A:L.48, A:F.93, D:R.18, D:W.37, D:F.40, D:Y.47, D:R.56, D:I.58, D:Y.61, D:W.66 Hydrogen bonds: A:N.94, D:H.59, D:S.60, D:Y.61, D:Y.61 pi-Stacking: A:F.39, A:F.39, D:Y.47 Halogen bonds: A: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

2025-10-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable global transcription activator SNF2L2

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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