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

Structure of DDB1 bound to DS15-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.36 Å

Oligo State

hetero-1-1-1-mer

Ligands

11 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:R.267 Salt bridges: A:H.265, A:R.267 SO4.2: 5 residues within 4Å: Chain A: K.564, Y.591, L.599, R.600, T.601 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.601, A:T.601 Salt bridges: A:K.564 SO4.3: 5 residues within 4Å: Chain A: E.575, F.576, N.577, T.616, G.618 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.575, A:N.577, A:T.616, A:G.618 SO4.4: 8 residues within 4Å: Chain A: S.466, S.467, S.468, H.505, R.547, V.549, F.551, T.560 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.467, A:S.468, A:T.560 Salt bridges: A:H.505, A:R.547 SO4.5: 5 residues within 4Å: Chain A: N.650, H.691, L.692, Q.693, E.694 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.650, A:L.692, A:Q.693, A:E.694 Salt bridges: A:H.691 SO4.6: 4 residues within 4Å: Chain A: R.133, S.200, L.201, R.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.200, A:L.201, A:R.202 Salt bridges: A:R.133, A:R.202 SO4.7: 2 residues within 4Å: Chain A: N.604, Y.606 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.604, A:N.604, A:Y.606 SO4.9: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.53, C:Y.53 Salt bridges: C:R.52, C:R.96 SO4.10: 5 residues within 4Å: Chain C: G.177, D.178, K.181, W.229 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.178, C:W.229 Salt bridges: C:K.181 SO4.11: 6 residues within 4Å: Chain C: K.181, F.224, E.225, E.228, W.229 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.225 Salt bridges: C:K.181 SO4.12: 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

1 x T6X: (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol(Non-covalent)

T6X.8: 27 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647, F.649 Chain B: I.25, G.26, E.27, Y.30, V.33, A.46, K.48, E.66, V.79, F.105, E.106, Y.107, M.108, D.109, H.110, D.111, S.155, N.156, L.158, A.168, D.169 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.25, B:Y.30, B:Y.30, B:V.33, B:F.105, B:Y.107, A:R.628, A:R.628 Hydrogen bonds: 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

2023-09-20

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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