SMTL ID : 9fjx.1

Crystal structure of human CRBN-DDB1 in complex with Lenalidomide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: G.56, M.57, 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.2: 6 residues within 4Å: Chain A: I.33, K.35, E.40, Y.42, F.323, F.353 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.35, A:Y.42, A:Y.42 Water bridges: A:S.331, A:F.353 EDO.3: 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.4: 4 residues within 4Å: Chain A: H.163, Q.183, D.184, P.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.183 EDO.9: 3 residues within 4Å: Chain B: Y.107, I.125, R.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.127

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: A.9, L.1012, V.1013, L.1029, L.1039, I.1139, H.1140, W.1141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.1141 pi-Cation interactions: A:W.1141, A:W.1141 DMS.6: 4 residues within 4Å: Chain A: E.784 Chain B: Q.190, K.191, K.194 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.784 DMS.10: 8 residues within 4Å: Chain B: W.229, L.253, P.254, I.255, I.279, M.280, C.283, I.302 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain B: C.288, C.291, C.356, C.359 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.288, B:C.291, B:C.356, B:C.359

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

LVY.8: 10 residues within 4Å: Chain B: N.316, P.317, H.318, H.322, H.343, S.344, W.345, W.351, W.365, F.367 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.316, B:W.351, B:W.351, B:W.365 Hydrogen bonds: B:N.316, B:H.343, B:H.343, B:W.345 Water bridges: B:E.342, B:E.342, B:E.342

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 1 residues within 4Å: Chain B: D.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chrisochoidou, Y. et al., Evaluating the impact of CRBN mutations on response to immunomodulatory drugs and novel cereblon E3 ligase modulators in myeloma. Blood (2025)

Release Date

2025-01-29

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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