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 CRBN-binding agents 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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