SMTL ID : 6hay.1 (1 other biounit)

Crystal structure of PROTAC 1 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 FX8: (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-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(Non-covalent)

FX8.1: 29 residues within 4Å: Chain A: V.38, F.39, L.42, P.43, L.48, Y.51, V.59, D.60, L.86, A.90, F.93, N.94, I.100 Chain B: 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 Ligands: EDO.4 24 PLIP interactions: 14 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:W.37, B:W.37, B:Y.47, B:I.58, B:I.58, B:Y.61, B:W.66, A:V.38, A:L.42, A:L.48, A:D.60, A:L.86, A:F.93 Hydrogen bonds: B:W.37, B:R.56, B:H.59, B:Y.61, B:H.64, A:N.94, A:N.94 Water bridges: B:Y.47 pi-Stacking: B:Y.47, A:F.39 Halogen bonds: A:N.94

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain B: R.31, R.110 Chain C: E.77 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.110, B:R.110, C:E.77 Water bridges: B:R.31, B:Q.113, C:E.77 EDO.3: 2 residues within 4Å: Chain B: G.72, H.74 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: Q.99 Chain B: R.57, I.58, H.59 Ligands: FX8.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.59, B:H.59 EDO.6: 5 residues within 4Å: Chain C: H.53, S.56, M.60, I.84 Chain D: F.93 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.56 EDO.7: 2 residues within 4Å: Chain C: N.70, S.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.72 EDO.8: 6 residues within 4Å: Chain C: N.46, F.47, R.48, E.49, I.50, F.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.48, C:E.49 EDO.9: 5 residues within 4Å: Chain D: D.40, E.41, R.80, A.81, D.82 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.40, D:D.82 EDO.10: 4 residues within 4Å: Chain D: Y.45, D.48, A.87, L.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.48, D:L.88 EDO.11: 4 residues within 4Å: Chain D: D.48, L.88, C.89, I.90 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.48, D:I.90, D:I.90 EDO.12: 4 residues within 4Å: Chain D: K.46, D.47, A.73, T.74 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.46, D:D.47, D:T.74 Water bridges: D:T.74, D:T.74 EDO.13: 5 residues within 4Å: Chain D: T.23, F.25, E.26, D.53, G.54 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.23, D:E.26

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 1 residues within 4Å: Chain B: R.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.159, B:R.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farnaby, W. et al., BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat.Chem.Biol. (2019)

Release Date

2019-06-12

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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