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

Structure of DDB1 bound to DS30-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 Ligands: SO4.8 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: K.564, R.600, T.601 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: S.466, S.467, S.468, H.505, R.547, V.549, 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: 3 residues within 4Å: Chain A: C.603, N.604, Y.606 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: V.23, T.24, N.266, T.319 Ligands: SO4.1, SO4.10 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: R.267, V.268, D.269, P.270 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: Y.175, R.267 Ligands: SO4.8 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: A.158, F.159, N.160 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: R.115 Chain B: R.242, R.273 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain A: R.133, P.180, V.199, S.200, L.201, R.202 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain B: R.275 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: P.282, S.283, A.284 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: R.242, K.267, K.268, Y.270 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: K.181, E.225, E.228, W.229 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: R.237, P.247, V.248, D.249 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: K.116, K.118, K.141 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: C.27, Y.29, W.30 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: R.55, R.59, D.195, C.198, L.261, Q.267 Ligand excluded by PLIP

1 x RWN: (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol(Non-covalent)

RWN.14: 26 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, G.28, 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 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.25, B:V.33, B:A.46, B:F.105, B:L.158, B:A.168, A:R.628 Hydrogen bonds: B:M.108, B:M.108, B:D.111

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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