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

Structure of DDB1 bound to Z7-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x RP9: ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide(Non-covalent)

RP9.1: 19 residues within 4Å: Chain A: N.607, I.609, R.628, R.647, F.649 Chain B: I.24, I.25, V.33, 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:F.649, B:L.158, B:L.158 pi-Cation interactions: A:R.628 Hydrogen bonds: B:Y.107, B:M.108, B:M.108

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

SO4.2: 6 residues within 4Å: Chain A: I.224, H.265, N.266, R.267, Y.275 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.266, A:R.267 Salt bridges: A:H.265 SO4.3: 3 residues within 4Å: Chain A: K.564, 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 SO4.4: 8 residues within 4Å: Chain A: S.466, S.467, S.468, H.505, R.547, V.549, F.551, T.560 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.466, A:S.466, A:S.467, A:S.468, A:R.547 Salt bridges: A:H.505 SO4.5: 2 residues within 4Å: Chain A: K.617, G.618 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.618 SO4.6: 3 residues within 4Å: Chain A: T.594, T.595, R.600 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.595, A:T.595 Salt bridges: A:R.600 SO4.7: 3 residues within 4Å: Chain A: C.603, N.604, Y.606 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.604, A:Y.606 SO4.8: 6 residues within 4Å: Chain A: C.22, V.23, T.24, N.266, T.319 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.22, A:T.24, A:N.266, A:T.319 SO4.9: 5 residues within 4Å: Chain A: P.180, V.199, S.200, L.201, R.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.200, A:L.201, A:R.202 Salt bridges: A:R.202 SO4.10: 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:N.650, A:Q.693, A:E.694 Salt bridges: A:H.691 SO4.11: 4 residues within 4Å: Chain A: T.722, T.724, Q.725, G.726 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.726 SO4.12: 3 residues within 4Å: Chain B: P.282, S.283, A.284 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.283, B:S.283, B:S.283, B:A.284 SO4.13: 7 residues within 4Å: Chain C: K.181, K.223, F.224, E.225, E.228, W.229 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.225, C:E.225 SO4.14: 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 SO4.15: 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 SO4.16: 5 residues within 4Å: Chain C: G.177, D.178, K.181, W.229 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.178, C:W.229 Salt bridges: C:K.181

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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