SMTL ID : 9cuo.2 (1 other biounit)

Crystal structure of CRBN with compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION

ZN.1: 4 residues within 4Å: Chain A: C.9, C.12, C.77, C.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.9, A:C.12, A:C.77, A:C.80 ZN.8: 4 residues within 4Å: Chain B: C.9, C.12, C.77, C.80 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.9, B:C.12, B:C.77, B:C.80 ZN.17: 4 residues within 4Å: Chain C: C.9, C.12, C.77, C.80 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.9, C:C.12, C:C.77, C:C.80

3 x 01: (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione

01.2: 8 residues within 4Å: Chain A: E.63, H.64, S.65, W.66, W.72, W.86, F.88 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.72, A:W.72, A:W.72, A:W.86 Hydrogen bonds: A:H.64, A:W.66 01.9: 9 residues within 4Å: Chain B: E.63, H.64, S.65, W.66, W.72, W.86, F.88 Ligands: EDO.11, EDO.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.63, B:W.66, B:W.72, B:W.72, B:W.72, B:W.86 Hydrogen bonds: B:H.64, B:W.66 01.18: 8 residues within 4Å: Chain C: E.63, H.64, S.65, W.66, W.72, W.86, F.88 Ligands: EDO.21 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.66, C:W.72, C:W.72, C:W.72, C:W.86 Hydrogen bonds: C:H.64, C:W.66

5 x SO4: SULFATE ION

SO4.3: 6 residues within 4Å: Chain A: K.50, K.87, K.99, W.101 Chain B: P.97, Q.98 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Water bridges: A:K.50, A:W.101 Salt bridges: A:K.50, A:K.87, A:K.99 Hydrogen bonds: B:Q.98, B:K.99 SO4.4: 7 residues within 4Å: Chain A: P.97, Q.98, K.99 Chain C: K.50, K.87, K.99, W.101 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Water bridges: C:K.50, C:K.50, C:A.51, C:K.99 Salt bridges: C:K.50, C:K.87, C:K.99 Hydrogen bonds: A:Q.98, A:K.99 SO4.10: 5 residues within 4Å: Chain A: K.50 Chain B: K.50, K.99 Chain C: K.50, K.99 8 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 3 interactions with chain C Water bridges: B:K.50, B:K.99, C:K.50, C:K.50 Salt bridges: B:K.50, B:K.99, A:K.50, C:K.50 SO4.19: 7 residues within 4Å: Chain B: K.50, K.87, K.99, W.101 Chain C: S.96, P.97, Q.98 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Water bridges: B:K.50, B:K.87, B:K.87, C:M.95 Salt bridges: B:K.50, B:K.87, B:K.99 Hydrogen bonds: C:Q.98 SO4.20: 1 residues within 4Å: Chain C: H.64 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.64, C:H.64 Salt bridges: C:H.64

10 x EDO: 1,2-ETHANEDIOL

EDO.5: 4 residues within 4Å: Chain A: W.72, V.74, W.86 Ligands: 01.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.86 EDO.6: 4 residues within 4Å: Chain A: E.16 Chain B: I.23, F.24, S.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.23 EDO.7: 5 residues within 4Å: Chain A: S.6, C.8, E.14, E.16 Chain B: S.25 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.6 Water bridges: A:E.14, A:E.14, B:S.25 EDO.11: 5 residues within 4Å: Chain B: W.72, V.74, H.83, W.86 Ligands: 01.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.86 EDO.12: 2 residues within 4Å: Chain B: H.43, E.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.43, B:H.43 EDO.13: 4 residues within 4Å: Chain B: W.66, W.86 Ligands: 01.9, EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain B: E.44, T.104, S.106 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.44, B:E.44, B:S.106 Water bridges: B:S.106 EDO.15: 6 residues within 4Å: Chain B: T.5, E.16, T.19 Chain C: I.23, F.24, S.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.16 EDO.16: 6 residues within 4Å: Chain B: F.24, S.25, L.26, V.42, T.45, T.47 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.24, B:L.26, B:V.42, B:T.47 Water bridges: B:T.47 EDO.21: 4 residues within 4Å: Chain C: W.72, V.74, W.86 Ligands: 01.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Discovery of KT-474─a Potent, Selective, and Orally Bioavailable IRAK4 Degrader for the Treatment of Autoimmune Diseases. J.Med.Chem. (2024)

Release Date

2024-08-28

Peptides

Protein cereblon: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Protein cereblon

Related Entries With Identical Sequence