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

Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 5 residues within 4Å: Chain A: K.564, R.589, Y.591, R.600, T.601 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.564, A:T.601 Salt bridges: A:K.564, A:K.564, A:R.589 CIT.4: 4 residues within 4Å: Chain C: R.52, Y.53, R.96, Q.135 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.53 Hydrogen bonds: C:Y.53, C:Q.135 Salt bridges: C:R.52, C:R.52, C:R.96, C:R.96

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

SO4.2: 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

1 x RKO: 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide(Non-covalent)

RKO.3: 17 residues within 4Å: Chain A: N.607, I.609, R.628, R.647, F.649 Chain B: I.24, I.25, A.46, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, L.158 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.158, B:L.158, A:R.628, A:F.649 Hydrogen bonds: B:M.108, B:M.108

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

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