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

Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CIT.1: 7 residues within 4Å: Chain A: Y.175, I.224, A.225, H.265, N.266, R.267, Y.275 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.225, A:N.266, A:R.267, A:Y.275 Salt bridges: A:H.265, A:H.265, A:R.267, A:R.267 CIT.3: 7 residues within 4Å: Chain C: R.52, Y.53, R.96, Y.97, V.131, Q.132, Q.135 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.135 Salt bridges: C:R.52, C:R.96, C:R.96, C:R.96

1 x RPW: 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide(Non-covalent)

RPW.2: 21 residues within 4Å: Chain A: N.607, I.609, R.628, R.647, D.648, F.649 Chain B: I.24, I.25, V.33, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, L.158, A.168 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:R.628, A:R.647, B:I.25, B:F.105 Hydrogen bonds: A:R.628, A:R.628, B:I.25, 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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