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

Structure of DDB1 bound to DS59-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.26 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.267 Salt bridges: A:H.265, A:R.267 SO4.2: 5 residues within 4Å: Chain A: K.564, Y.591, L.599, R.600, T.601 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.601, A:T.601, A:T.601 Salt bridges: A:K.564 SO4.3: 6 residues within 4Å: Chain A: R.133, P.180, V.199, S.200, L.201, R.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.199, A:L.201, A:R.202 Salt bridges: A:R.133, A:R.202 SO4.5: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.52, C:Y.53, C:Y.53 Salt bridges: C:R.96 SO4.6: 4 residues within 4Å: Chain C: R.237, P.247, V.248, D.249 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.248 Salt bridges: C:R.237

1 x RMX: 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide(Non-covalent)

RMX.4: 27 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647 Chain B: I.25, G.26, E.27, G.28, T.29, 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 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.29, B:A.46, B:K.48, B:F.105, B:F.105, B:Y.107, A:R.628 Hydrogen bonds: B:E.27, B:M.108, B:M.108, B:S.155, A:R.628

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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