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

Structure of DDB1 bound to 919278-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CIT.1: 6 residues within 4Å: Chain A: T.24, I.224, H.265, N.266, R.267, Y.275 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.265, A:N.266, A:N.266, A:R.267 Salt bridges: A:H.265, A:R.267, A:R.267 CIT.3: 7 residues within 4Å: Chain C: R.52, Y.53, R.96, Y.97, V.131, Q.132, Q.135 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.53, C:Y.53, C:Q.135 Salt bridges: C:R.52, C:R.96, C:R.96 CIT.4: 5 residues within 4Å: Chain C: Y.72, Q.183, V.186, Q.187, W.190 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.190, C:W.190

1 x RVH: (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide(Non-covalent)

RVH.2: 18 residues within 4Å: Chain A: N.607, I.609, R.628, R.647, F.649 Chain B: I.25, V.33, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, L.158 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:R.628, B:I.25, B:V.33, B:A.46, B:F.105, B:L.158 Hydrogen bonds: B:Y.107, 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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