SMTL ID : 8bua.1 (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

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

CIT.1: 7 residues within 4Å: Chain A: T.24, I.224, A.225, H.265, N.266, R.267, Y.275 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.266, A:Y.275, A:Y.275 Salt bridges: A:H.265, 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 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.53, C:R.96, C:R.96, C:Q.135 Salt bridges: C:R.52, C:R.96, C:R.96

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

RVH.2: 19 residues within 4Å: Chain A: N.607, R.628, R.647, F.649 Chain B: I.25, V.33, K.35, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, L.158, A.168 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.46, B:V.79, B:F.105, B:F.105, B:L.158, A:R.628 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
A

B
B

C
C

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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