SMTL ID : 9d0v.1

Crystal structure of CDK2/CyclinE1 in complex with Cpd 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: 6-chloro-8-cyclopentyl-2-[4-(ethanesulfonyl)-2-methylanilino]pyrido[2,3-d]pyrimidin-7(8H)-one

01.1: 14 residues within 4Å: Chain A: I.10, G.13, V.18, A.31, F.80, E.81, F.82, L.83, H.84, Q.85, D.86, K.89, Q.131, L.134 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.10, A:I.10, A:V.18, A:A.31, A:F.80, A:F.82, A:L.134 Hydrogen bonds: A:L.83, A:L.83

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain B: I.55, L.56, W.59, L.96, Q.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.93 Water bridges: B:L.96

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain B: T.94, L.98, A.128, E.133 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.94, B:G.127, B:A.128 GOL.4: 6 residues within 4Å: Chain B: R.37, Q.39, L.200, E.201, F.202, P.203 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.37, B:R.37, B:L.200, B:F.202, B:Y.204 GOL.5: 1 residues within 4Å: Ligands: EDO.7 No protein-ligand interaction detected (PLIP)

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

EDO.6: 2 residues within 4Å: Chain B: H.214, R.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.214, B:R.247 EDO.7: 2 residues within 4Å: Chain B: M.140 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: R.150, A.151, F.152, G.153 Chain B: E.72, E.111 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.150, A:F.152, B:E.111 Water bridges: A:R.122

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclin-dependent kinase 2

G1/S-specific cyclin-E1

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