SMTL ID : 7bqv.1

Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x F4U: 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione(Non-covalent)

F4U.1: 16 residues within 4Å: Chain A: N.34, P.35, H.36, E.60, H.61, S.62, W.63, W.69, W.83, F.85 Chain B: V.3, C.4, S.5, V.6, C.7, G.8 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.35, A:W.69, A:W.69, B:V.3 Hydrogen bonds: A:N.34, A:H.61, A:H.61, A:W.63

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.6, C.9, C.74, C.77 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.6, A:C.9, A:C.74, A:C.77 ZN.4: 4 residues within 4Å: Chain B: C.4, C.7, H.20, H.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4, B:C.7, B:H.20, B:H.24

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: I.20, S.22, P.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.20 Water bridges: A:S.22 SO4.5: 4 residues within 4Å: Chain B: F.11, T.12, T.13, N.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.12, B:T.12, B:T.13, B:N.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furihata, H. et al., Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide. Nat Commun (2020)

Release Date

2020-08-26

Peptides

Protein cereblon: A
Sal-like protein 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein cereblon

Sal-like protein 4