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

Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CIT.1: 7 residues within 4Å: Chain A: E.69, I.224, A.225, H.265, N.266, R.267, Y.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.266, A:N.266, A:R.267 Salt bridges: A:H.265, A:R.267, A:R.267 CIT.2: 7 residues within 4Å: Chain B: R.52, Y.53, R.96, Y.97, V.131, Q.132, Q.135 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.53, B:Q.132 Salt bridges: B:R.52, B:R.52, B:R.96, B:R.96 CIT.3: 6 residues within 4Å: Chain B: K.181, K.223, F.224, E.225, E.228, W.229 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.224, B:W.229 Hydrogen bonds: B:K.223, B:E.225, B:W.229

1 x RNU: ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide(Non-covalent)

RNU.4: 20 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647 Chain C: I.25, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, L.158, A.168, D.169, R.174 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.105 Hydrogen bonds: C:Y.107, C:M.108, C:M.108, C:M.108, A:R.628 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-K: B
Cyclin-dependent kinase 12: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

C
E

DNA damage-binding protein 1

Cyclin-K

Cyclin-dependent kinase 12

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