SMTL ID : 7z77.1

Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x IFF: (2~{S},4~{R})-~{N}-[(1~{S})-4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]butyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

IFF.1: 35 residues within 4Å: Chain C: N.16, S.17, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, T.49, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: V.38, F.39, Q.41, L.42, P.43, E.47, L.48, Y.51, V.59, D.60, F.61, L.86, N.89, A.90, F.93, N.94, I.100 25 PLIP interactions: 15 interactions with chain C, 10 interactions with chain D Hydrophobic interactions: C:R.18, C:W.37, C:Y.47, C:P.48, C:I.58, C:I.58, C:Y.61, C:W.66, D:V.38, D:L.42, D:L.48, D:L.48, D:D.60, D:F.93, D:I.100 Hydrogen bonds: C:Y.47, C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64, D:N.94 pi-Stacking: C:Y.47, D:F.39 Halogen bonds: D: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

2022-09-14

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
A

B
B

C
C

D
D

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Probable global transcription activator SNF2L2

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