SMTL ID : 7z6l.1

Crystal structure of PROTAC 5 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x IEI: (2~{S},4~{R})-~{N}-[[2-[3-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propoxy]-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)

IEI.1: 29 residues within 4Å: Chain A: V.38, F.39, Q.41, L.42, P.43, E.47, L.48, Y.51, V.59, D.60, L.86, N.89, A.90, F.93, N.94, I.100 Chain B: F.25, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 21 PLIP interactions: 11 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.38, A:L.42, A:L.48, A:D.60, A:F.93, A:I.100, B:Y.47, B:I.58, B:Y.61, B:W.66 Hydrogen bonds: A:Y.51, A:N.94, B:R.56, B:H.59, B:S.60, B:Y.61, B:H.64 Salt bridges: A:E.47 pi-Stacking: A:F.39, B:Y.47 Halogen bonds: A:L.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kofink, C. et al., A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. Nat Commun (2022)

Release Date

2022-09-07

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable global transcription activator SNF2L2

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

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