SMTL ID : 6td3.1 (2 other biounits)

Structure of DDB1 bound to CR8-engaged CDK12-cyclinK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.46 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x RC8: (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol(Non-covalent)

RC8.1: 26 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647, F.649 Chain B: I.25, G.26, G.28, V.33, K.35, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, S.155, N.156, L.158, A.168, D.169 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.25, B:V.33, B:A.46, B:K.48, B:F.105, B:Y.107, A:R.628 Hydrogen bonds: B:M.108, B:M.108, B:D.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slabicki, M. et al., The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature (2020)

Release Date

2020-06-17

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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