SMTL ID : 8ou6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.6, Q.8, C.9, Q.11, C.72, Q.74, C.75, S.77 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.6, A:C.9, A:C.72, A:C.75 ZN.5: 7 residues within 4Å: Chain B: C.6, Q.8, C.9, C.72, Q.74, C.75, S.77 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.6, B:C.9, B:C.72, B:C.75 ZN.9: 8 residues within 4Å: Chain C: C.6, Q.8, C.9, Q.11, C.72, Q.74, C.75, S.77 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.6, C:C.9, C:C.72, C:C.75

2 x W26: 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-methyl-benzamide(Non-covalent)

W26.2: 10 residues within 4Å: Chain A: N.32, P.33, A.34, E.58, F.59, S.60, W.61, W.67, W.81, Y.83 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.59, A:W.61, A:W.67, A:W.67, A:W.81 Hydrogen bonds: A:N.32, A:F.59, A:W.61, A:Y.83 Water bridges: A:W.81, A:W.81 W26.6: 11 residues within 4Å: Chain B: N.32, P.33, A.34, M.36, F.38, F.59, S.60, W.61, W.67, W.81, Y.83 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.33, B:F.59, B:W.61, B:W.67, B:W.67, B:W.81 Hydrogen bonds: B:N.32, B:F.59, B:W.61

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

PO4.3: 3 residues within 4Å: Chain A: Q.88, P.89, Q.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.88, A:Q.88, A:Q.90 PO4.4: 10 residues within 4Å: Chain A: F.4, W.41, K.97, D.98, L.100, A.101, E.102 Chain B: E.27, H.28, V.29 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.97, A:K.97, A:E.102, B:V.29 Water bridges: A:K.97 Salt bridges: A:K.97 PO4.7: 3 residues within 4Å: Chain B: G.35, M.36, I.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.37, B:I.37 PO4.8: 4 residues within 4Å: Chain C: Q.11, T.12, Q.47, G.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.11

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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