SMTL ID : 7z76.1

Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.2: 1 residues within 4Å: Chain C: R.57 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain C: R.56 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain C: I.58, H.59 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain C: Q.45 Chain D: Q.99, I.100 Ligands: IFJ.5 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain D: E.66, N.70, K.72 Ligand excluded by PLIP

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

IFJ.5: 29 residues within 4Å: Chain C: N.16, R.18, F.25, W.37, F.40, Y.47, P.48, 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, L.86, A.90, F.93, N.94, I.100 Ligands: IOD.6 23 PLIP interactions: 9 interactions with chain D, 14 interactions with chain C Hydrophobic interactions: D:V.38, D:P.43, D:L.48, D:F.93, C:R.18, C:W.37, C:W.37, C:Y.47, C:I.58, C:H.59, C:Y.61, C:W.66 Hydrogen bonds: D:N.94, C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64 Salt bridges: D:E.47 pi-Stacking: D:F.39, D:Y.51, C:Y.47 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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