SMTL ID : 6hay.2 (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: 28 residues within 4Å: Chain A: V.38, F.39, Q.41, L.42, L.48, Y.51, V.59, D.60, A.90, F.93, N.94, I.100 Chain B: N.16, R.18, P.35, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Ligands: EDO.4, EDO.5 22 PLIP interactions: 8 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:L.42, A:L.48, A:D.60, A:F.93, B:W.37, B:W.37, B:F.40, B:Y.47, B:I.58, B:Y.61, B:W.66 Hydrogen bonds: A:N.94, A:N.94, B:W.37, B:R.56, B:H.59, B:Y.61, B:Y.61, B:H.64 pi-Stacking: A:F.39, B:Y.47 Halogen bonds: A:N.94

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

EDO.2: 2 residues within 4Å: Chain B: P.30 Chain C: E.77 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Water bridges: B:P.30, B:R.31, B:R.110, C:E.77 Hydrogen bonds: C:E.77 EDO.3: 6 residues within 4Å: Chain B: T.73, D.75, Q.113, R.116, S.117, P.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.75, B:R.116 EDO.4: 6 residues within 4Å: Chain A: Q.99 Chain B: R.57, I.58, H.59 Ligands: FX8.1, EDO.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.59 EDO.5: 7 residues within 4Å: Chain A: S.98, Q.99, I.100 Chain B: H.59, Y.61 Ligands: FX8.1, EDO.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.99, A:I.100, B:Y.61 EDO.7: 5 residues within 4Å: Chain C: E.49, I.50, E.87, M.90, A.91 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain B: R.28, S.29, P.30 Chain C: E.74, I.75, P.76 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.74, C:I.75 Water bridges: C:E.74, C:I.75, C:E.77, B:S.29 EDO.9: 3 residues within 4Å: Chain C: S.71, S.72, T.73 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.72, C:S.72, C:T.73, C:T.73, C:T.73 Water bridges: C:S.72, B:Q.81 EDO.10: 4 residues within 4Å: Chain D: D.48, Q.49, L.50 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.50 EDO.11: 4 residues within 4Å: Chain D: K.46, D.47, A.73, T.74 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.74, D:T.74 Water bridges: D:P.72, D:T.74 EDO.12: 2 residues within 4Å: Chain D: M.6, F.93 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.56 EDO.13: 4 residues within 4Å: Chain D: Y.45, D.48, L.88 Ligands: EDO.10 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 4 residues within 4Å: Chain B: D.128, I.129, V.130, R.131 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.131 Water bridges: B:S.132 Salt bridges: B:D.128, B:D.128, B:R.131

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
E

B
F

C
G

D
H

Probable global transcription activator SNF2L2

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

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