SMTL ID : 9cuo.1 (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.6: 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.12: 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 01.7: 8 residues within 4Å: Chain B: E.63, H.64, S.65, W.66, W.72, W.86, F.88 Ligands: EDO.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.72, B:W.72, B:W.72, B:W.86 Hydrogen bonds: B:H.64, B:W.66 01.13: 7 residues within 4Å: Chain C: E.63, H.64, S.65, W.66, W.72, W.86, F.88 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:H.64, C:W.72, C:W.72, C:W.72, C:W.86 Hydrogen bonds: C:H.64, C:W.66

8 x SO4: SULFATE ION

SO4.3: 7 residues within 4Å: Chain A: K.50, K.87, K.99, W.101 Chain B: S.96, P.97, Q.98 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Water bridges: A:K.50, A:K.50, A:A.51 Salt bridges: A:K.50, A:K.87, A:K.99 Hydrogen bonds: B:Q.98 SO4.4: 4 residues within 4Å: Chain A: V.42, T.45, W.66, F.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.42, A:T.45 SO4.8: 7 residues within 4Å: Chain B: K.50, K.87, K.99, W.101 Chain C: S.96, P.97, Q.98 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Water bridges: B:W.101 Salt bridges: B:K.50, B:K.87, B:K.99, C:K.99 Hydrogen bonds: C:Q.98, C:K.99 SO4.9: 1 residues within 4Å: Chain B: H.64 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.64 SO4.10: 7 residues within 4Å: Chain B: T.5, S.6, E.16, T.19 Chain C: I.23, F.24, S.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.5, B:E.16 SO4.14: 5 residues within 4Å: Chain A: K.50, K.99 Chain B: K.50 Chain C: K.50, K.99 9 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B, 4 interactions with chain C Water bridges: A:K.50, A:K.50, C:K.50, C:K.50 Salt bridges: A:K.50, A:K.99, B:K.50, C:K.50, C:K.99 SO4.15: 7 residues within 4Å: Chain A: P.97, Q.98, K.99 Chain C: K.50, K.87, K.99, W.101 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:Q.98, A:K.99 Water bridges: A:M.95, C:K.50, C:K.50, C:K.87, C:K.87 Salt bridges: C:K.50, C:K.87, C:K.99 SO4.16: 1 residues within 4Å: Chain C: H.64 2 PLIP interactions: 2 interactions with chain C Water bridges: C:H.64 Salt bridges: C:H.64

2 x EDO: 1,2-ETHANEDIOL

EDO.5: 5 residues within 4Å: Chain A: W.72, V.74, H.83, W.86 Ligands: 01.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.86 EDO.11: 5 residues within 4Å: Chain B: W.72, V.74, H.83, W.86 Ligands: 01.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B: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
A

B
B

C
C

Protein cereblon

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