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

Structure of DDB1 bound to DS08-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.266, A:R.267 Salt bridges: A:H.265 SO4.2: 4 residues within 4Å: Chain A: K.564, L.599, 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 SO4.3: 5 residues within 4Å: Chain A: N.650, H.691, L.692, Q.693, E.694 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.650, A:E.694 Salt bridges: A:H.691 SO4.5: 6 residues within 4Å: Chain B: K.133, E.137, V.315, E.316, L.317, S.318 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.317 SO4.6: 4 residues within 4Å: Chain C: R.237, P.247, V.248, D.249 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.248, C:D.249 Salt bridges: C:R.237 SO4.7: 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 SO4.8: 5 residues within 4Å: Chain C: K.181, F.224, E.225, E.228, W.229 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.225, C:W.229 Salt bridges: C:K.181

1 x RWE: (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol(Non-covalent)

RWE.4: 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, A.46, K.48, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, S.155, L.158, A.168 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.25, B:I.25, B:V.33, B:A.46, B:V.79, B:F.105, B:L.158, A:I.609, A:R.628 Hydrogen bonds: B:M.108, B:M.108, B:D.111 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
G

B
H

C
I

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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