SMTL ID : 8bur.2 (2 other biounits)

Structure of DDB1 bound to DS50-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.64 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 10 residues within 4Å: Chain A: F.386, K.387, Y.418, E.419, S.420, R.439, I.440, L.452, R.453, S.455 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.420, A:I.440 Salt bridges: A:R.453 SO4.2: 2 residues within 4Å: Chain A: N.604, Y.606 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.606 SO4.3: 7 residues within 4Å: Chain A: I.224, A.225, H.265, N.266, R.267, Y.275 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.267, A:R.267 Salt bridges: A:H.265 SO4.4: 6 residues within 4Å: Chain A: C.22, V.23, T.24, N.266, T.319 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.22, A:T.24, A:T.24, A:N.266, A:T.319 SO4.5: 3 residues within 4Å: Chain A: T.356, F.357, T.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.356, A:T.358 SO4.6: 8 residues within 4Å: Chain A: S.466, S.467, S.468, H.505, R.547, V.549, F.551, T.560 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.466, A:S.466, A:S.467, A:S.468, A:T.560, A:E.563 Salt bridges: A:H.505, A:R.547 SO4.7: 4 residues within 4Å: Chain A: K.564, Y.591, 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 SO4.9: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.53 Salt bridges: C:R.52, C:R.96 SO4.10: 2 residues within 4Å: Chain C: H.89, F.94 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.89 SO4.11: 4 residues within 4Å: Chain C: G.177, D.178, K.181, W.229 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.178, C:W.229

1 x RQU: ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide(Non-covalent)

RQU.8: 25 residues within 4Å: Chain A: N.607, I.609, R.628, R.647, F.649 Chain B: I.24, I.25, G.26, E.27, V.33, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, K.153, S.155, L.158, A.168, D.169 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.25, B:V.33, B:F.105, A:R.628, A:R.628, A:F.649 Hydrogen bonds: B:M.108, B:M.108 pi-Cation interactions: 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
A

B
B

C
C

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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