SMTL ID : 9sfm.1

Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: I.33, K.35, E.40, Y.42, F.323, F.353 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.35, A:Y.42, A:Y.42 EDO.2: 5 residues within 4Å: Chain A: G.329, D.330, E.384, R.388, P.716 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.330, A:E.384 Water bridges: A:E.384, A:G.385 EDO.3: 5 residues within 4Å: Chain A: G.56, Y.58, K.1063, S.1064, V.1065 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.1065 Water bridges: A:G.56, A:Y.58, A:Y.58, A:S.1064 EDO.4: 7 residues within 4Å: Chain A: Q.727, V.729, S.730, N.826, T.827, Q.852, Y.853 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.730, A:N.826, A:T.827, A:Q.852 Water bridges: A:Q.727 EDO.5: 5 residues within 4Å: Chain A: N.16, A.62, V.63, M.64, E.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:M.64, A:E.65 EDO.7: 4 residues within 4Å: Chain B: S.150, Q.153, E.155, N.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.155, B:N.158

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain B: C.278, C.281, C.346, C.349 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.278, B:C.281, B:C.346, B:C.349

1 x LVY: S-Lenalidomide(Non-covalent)

LVY.8: 10 residues within 4Å: Chain B: N.306, P.307, H.308, H.312, H.333, S.334, W.335, W.341, W.355, F.357 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.306, B:P.307, B:W.335, B:W.341, B:W.341, B:W.355, B:F.357 Hydrogen bonds: B:N.306, B:H.333, B:H.333, B:W.335 Water bridges: B:E.332

1 x 01: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea

01.9: 18 residues within 4Å: Chain B: L.216, W.219, L.223, L.228, R.238, V.239, C.242, L.243, P.244, I.269, C.273, L.276, K.289, I.292, S.294, L.297, C.298, P.300 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.219, B:W.219, B:L.223, B:L.228, B:L.243, B:P.244, B:I.269, B:L.276, B:K.289, B:I.292 Hydrogen bonds: B:R.238, B:S.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, C., : Identification of an allosteric site on the E3 ligase adapter cereblon. To Be Published

Release Date

2025-11-19

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA damage-binding protein 1

Protein cereblon

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