SMTL ID : 8bu3.1 (2 other biounits)

Structure of DDB1 bound to DS19-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: C.603, N.604, Y.606 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.604, A:N.604, A:Y.606

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

SO4.2: 5 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.265, A:N.266, A:R.267 Salt bridges: A:H.265, A:R.267 SO4.3: 5 residues within 4Å: Chain A: K.564, Y.591, L.599, R.600, T.601 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.601 Salt bridges: A:K.564 SO4.4: 4 residues within 4Å: Chain A: R.133, S.200, L.201, R.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.201, A:R.202 Salt bridges: A:R.133, A:R.202 SO4.6: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.53, C:Y.53 Salt bridges: C:R.52, C:R.96 SO4.7: 4 residues within 4Å: Chain C: G.177, D.178, K.181, W.229 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.178, C:W.229 Salt bridges: C:K.181 SO4.8: 4 residues within 4Å: Chain C: R.237, P.247, V.248, D.249 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.248, C:D.249 Salt bridges: C:R.237

1 x RSI: 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine(Non-covalent)

RSI.5: 25 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647 Chain B: I.24, I.25, G.26, E.27, 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, L.158, A.168 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.25, B:V.33, B:A.46, B:K.48, B:F.105, B:Y.107, B:A.168, A:I.609, A:R.628 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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