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

Structure of DDB1 bound to Z11-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

16 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 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: K.564, R.600, T.601 Ligand excluded by PLIP SO4.3: 9 residues within 4Å: Chain A: V.465, S.466, S.467, S.468, H.505, R.547, V.549, F.551, T.560 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: K.617, G.618 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: T.594, T.595, R.600 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: K.423, S.572, L.612, Y.613, L.614, K.615 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: N.604, Y.606 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: C.22, V.23, T.24, N.266, T.319 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: P.180, V.199, S.200, L.201, R.202 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: N.650, H.691, L.692, Q.693, E.694 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: R.275, L.286 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: P.282, S.283, A.284 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain C: K.181, F.224, E.225, E.228, W.229 Ligands: SO4.17 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: 5 residues within 4Å: Chain C: G.177, D.178, K.181, W.229 Ligands: SO4.14 Ligand excluded by PLIP

1 x RVU: ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide(Non-covalent)

RVU.11: 23 residues within 4Å: Chain A: N.607, N.608, I.609, M.627, R.628, R.647, F.649 Chain B: I.24, I.25, G.26, 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 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:R.628, A:F.649, B:A.46, B:F.105, B:L.158 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

2023-09-13

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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