SMTL ID : 8buq.1 (2 other biounits)

Structure of DDB1 bound to DS43-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CIT.1: 9 residues within 4Å: Chain A: E.69, K.172, Y.175, I.224, A.225, H.265, N.266, R.267, Y.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.265, A:R.267 Salt bridges: A:R.267, A:R.267 CIT.3: 5 residues within 4Å: Chain C: R.52, Y.53, R.96, V.131, Q.135 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.53 Hydrogen bonds: C:R.96, C:Q.135 Salt bridges: C:R.52, C:R.96

1 x RQ9: (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol(Non-covalent)

RQ9.2: 26 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647 Chain B: I.25, E.27, G.28, V.33, K.35, A.46, K.48, E.66, 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 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.25, B:I.25, B:V.33, B:V.33, B:A.46, B:K.48, B:V.79, B:F.105, B:F.105, B:D.111, A:I.609 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
A

B
B

C
C

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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