SMTL ID : 8ou5.1

Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.25, Q.27, C.28, Q.30, C.91, Q.93, C.94, S.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.25, A:C.28, A:C.91, A:C.94 ZN.3: 6 residues within 4Å: Chain B: C.25, C.28, C.91, Q.93, C.94, S.96 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.25, B:C.28, B:C.91, B:C.94 ZN.5: 8 residues within 4Å: Chain C: C.25, Q.27, C.28, Q.30, C.91, Q.93, C.94, S.96 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.25, C:C.28, C:C.91, C:C.94

2 x W1X: 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-(trifluoromethyl)benzamide(Non-covalent)

W1X.2: 12 residues within 4Å: Chain A: N.51, P.52, A.53, F.57, F.78, S.79, W.80, W.86, I.88, H.97, W.100, Y.102 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.51, A:W.80, A:W.86, A:W.86, A:W.100 Hydrogen bonds: A:N.51, A:F.78, A:W.80, A:Y.102 W1X.4: 12 residues within 4Å: Chain B: N.51, P.52, A.53, F.57, F.78, S.79, W.80, W.86, I.88, H.97, W.100, Y.102 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.80, B:W.86, B:W.86, B:W.100 Hydrogen bonds: B:N.51, B:F.78, B:W.80, B:W.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinebach, C. et al., Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. J.Med.Chem. (2023)

Release Date

2023-11-15

Peptides

Cereblon isoform 4: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Cereblon isoform 4

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