SMTL ID : 8bu5.3 (2 other biounits)

Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 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, A:R.267 Salt bridges: A:H.265 SO4.3: 3 residues within 4Å: Chain B: K.153, S.155, T.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.155, B:T.190, B:T.190 Salt bridges: B:K.153

1 x RMF: ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine(Non-covalent)

RMF.2: 24 residues within 4Å: Chain A: N.607, R.628, R.647 Chain B: I.25, G.26, E.27, V.33, K.35, A.46, K.48, E.66, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, M.113, S.155, L.158, A.168, D.169 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B pi-Cation interactions: A:R.628 Hydrophobic interactions: B:I.25 Hydrogen bonds: B:M.108, B:M.108, B:D.111

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

CIT.4: 4 residues within 4Å: Chain C: R.52, Y.53, R.96, Q.135 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.53, C:R.96, C:R.96, C:Q.135 Salt bridges: C:R.52, C:R.96, C:R.96

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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