SMTL ID : 8bu2.2 (2 other biounits)

Structure of DDB1 bound to DS18-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

RVQ.1: 24 residues within 4Å: Chain A: N.607, N.608, I.609, R.628, R.647 Chain B: I.25, G.26, E.27, V.33, K.35, 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, D.169 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.25, B:I.25, B:A.46, B:F.105, B:L.158, B:A.168, A:I.609 Hydrogen bonds: B:M.108, B:M.108 Halogen bonds: A:N.607, A:R.647

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

SO4.2: 5 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: K.564, R.600, T.601 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: S.466, S.467, S.468, H.505, R.547, V.549, F.551, T.560 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: K.617, G.618 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: N.650, H.691, L.692, Q.693, E.694 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: T.594, T.595, R.600 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: K.423, S.572, L.612, Y.613, L.614, K.615 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: C.603, N.604, Y.606 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: R.802, Q.806, T.825, A.826, D.827 Ligand excluded by PLIP SO4.11: 1 residues within 4Å: Chain B: R.275 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: P.282, S.283, A.284 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain C: G.177, D.178, K.181, W.229 Ligands: SO4.14 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain C: K.181, K.223, F.224, E.225, E.228, W.229 Ligands: SO4.13 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain C: R.237, P.247, V.248, D.249 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: F.88, H.89, S.90, F.94 Ligand excluded by PLIP

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
D

B
E

C
F

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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