SMTL ID : 9d0x.1

Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 (local mask)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.286, C.289, T.292, C.354, C.357 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.286, A:C.289, A:C.354, A:C.357

1 x 01: (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione

01.2: 22 residues within 4Å: Chain A: N.314, P.315, E.340, H.341, S.342, W.343, W.349, W.363, F.365 Chain B: I.10, V.18, A.31, V.64, F.80, E.81, F.82, L.83, Q.85, D.86, K.89, Q.131, L.134 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.10, B:V.18, B:A.31, B:V.64, B:F.80, B:F.80, B:F.82, B:L.134, A:P.315, A:H.341, A:W.343, A:W.343, A:W.349 Hydrogen bonds: B:L.83, B:L.83, A:N.314, A:W.343 Salt bridges: A:E.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwiatkowski, N. et al., CDK2 heterobifunctional degraders co-degrade CDK2 and cyclin E resulting in efficacy in CCNE1-amplified and overexpressed cancers. Cell Chem Biol (2025)

Release Date

2025-04-16

Peptides

Protein cereblon: A
Cyclin-dependent kinase 2: B
G1/S-specific cyclin-E1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Protein cereblon

Cyclin-dependent kinase 2

G1/S-specific cyclin-E1

Related Entries With Identical Sequence