SMTL ID : 8ou3.1

Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.25, C.28, C.91, C.94 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.25, A:C.28, A:C.91, A:C.94 ZN.4: 4 residues within 4Å: Chain B: C.25, C.28, C.91, C.94 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.25, B:C.28, B:C.91, B:C.94 ZN.7: 4 residues within 4Å: Chain C: C.25, C.28, C.91, C.94 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.25, C:C.28, C:C.91, C:C.94

2 x EF2: S-Thalidomide(Non-covalent)

EF2.2: 9 residues within 4Å: Chain A: N.51, P.52, E.77, F.78, S.79, W.80, W.86, W.100, Y.102 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.51, A:P.52, 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 EF2.8: 6 residues within 4Å: Chain C: F.78, S.79, W.80, W.86, W.100, Y.102 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.80, C:W.86, C:W.100, C:W.100 Hydrogen bonds: C:F.78, C:W.80

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: M.55, F.57, H.97, R.118 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.97, A:R.118 PO4.6: 3 residues within 4Å: Chain B: F.57, H.97, R.118 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.97, B:R.118 PO4.9: 2 residues within 4Å: Chain C: H.97, R.118 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.97, C:R.118

1 x W1T: 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-fluoranyl-benzamide(Non-covalent)

W1T.5: 8 residues within 4Å: Chain B: N.51, P.52, F.78, S.79, W.80, W.86, W.100, Y.102 7 PLIP interactions: 7 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

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

Related Entries With Identical Sequence