SMTL ID : 8bu1.3 (2 other biounits)

Structure of DDB1 bound to DS17-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.265, A:H.265, A:N.266, A:R.267 GOL.3: 8 residues within 4Å: Chain A: R.780 Chain B: M.113, K.153, C.154, S.155, T.190, W.192, Y.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.154, B:S.155 GOL.4: 5 residues within 4Å: Chain B: R.272, R.275, D.290, H.291, T.294 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.290, B:T.294 GOL.5: 4 residues within 4Å: Chain C: R.52, Y.53, R.96, Q.135 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.52, C:R.52, C:R.96, C:R.96, C:Q.135 GOL.6: 5 residues within 4Å: Chain C: K.181, F.224, E.225, E.228, W.229 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.181, C:E.225

1 x RQL: (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol(Non-covalent)

RQL.2: 23 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, V.33, K.35, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, L.158, A.168 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.25, B:I.25, B:V.33, B:A.46, B:K.48, B:F.105, B:L.158, B:A.168, A:I.609 Hydrogen bonds: B:M.108, B:M.108, B:D.111 Halogen bonds: A:N.607

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
G

B
H

C
I

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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