SMTL ID : 8buh.2 (2 other biounits)

Structure of DDB1 bound to WX3-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.79 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.266, A:R.267 Salt bridges: A:H.265, A:R.267 SO4.2: 4 residues within 4Å: Chain A: K.564, L.599, R.600, T.601 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.601, A:T.601, A:T.601 Salt bridges: A:K.564 SO4.4: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.53 Salt bridges: C:R.52, C:R.96

1 x RR9: 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one(Non-covalent)

RR9.3: 23 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647 Chain B: I.25, G.26, G.28, V.33, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, S.155, L.158, A.168, D.169 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.25, B:I.25, B:V.33, B:A.46, B:K.48, B:V.79, B:F.105, B:F.105, A:R.628 Hydrogen bonds: B:Y.107, B:M.108, B:M.108, B:D.109, B:S.155, A:R.628 pi-Cation interactions: A:R.628

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozicka, Z. et al., Design principles for cyclin K molecular glue degraders. Nat.Chem.Biol. (2024)

Release Date

2023-09-13

Peptides

DNA damage-binding protein 1: A
Cyclin-dependent kinase 12: B
Cyclin-K: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

Related Entries With Identical Sequence