SMTL ID : 6xk9.1 (1 other biounit)

Cereblon in complex with DDB1, CC-90009, and GSPT1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.64 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x V4M: 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide(Non-covalent)

V4M.1: 20 residues within 4Å: Chain A: Q.99, V.101, D.136, K.137, K.138, S.139, G.140, I.191, G.192, K.193 Chain C: N.315, P.316, H.317, E.341, H.342, S.343, W.344, W.350, W.364, F.366 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:P.316, C:W.344, C:W.350, C:W.350, C:F.366, A:K.193, A:K.193 Hydrogen bonds: C:N.315, C:E.341, C:H.342, C:H.342, C:W.344, A:Q.99

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain C: C.287, C.290, C.355, C.358, S.360 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.287, C:C.290, C:C.355, C:C.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Surka, C. et al., CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Blood (2021)

Release Date

2020-12-02

Peptides

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A: A
DNA damage-binding protein 1: B
Protein cereblon: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
Y

C
Z

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A

DNA damage-binding protein 1

Protein cereblon

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