SMTL ID : 8oiz.1

Crystal structure of human CRBN-DDB1 in complex with Pomalidomide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: I.33, K.35, E.40, Y.42, F.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35, A:Y.42 EDO.2: 6 residues within 4Å: Chain A: G.56, M.57, Y.58, K.1063, S.1064, V.1065 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1064, A:V.1065 Water bridges: A:Y.58 EDO.3: 5 residues within 4Å: Chain A: G.329, D.330, E.384, R.388, P.716 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.330 Water bridges: A:E.384, A:L.717 EDO.4: 4 residues within 4Å: Chain A: I.88, A.104, D.146, N.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.149 EDO.5: 5 residues within 4Å: Chain A: E.160, E.161, L.162, H.163, D.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.184, A:D.184 Water bridges: A:H.163 EDO.6: 6 residues within 4Å: Chain A: I.100, I.101, T.102, S.1064, V.1065, K.1067 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.102, A:T.102, A:S.1064, A:K.1067

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 Y70: S-Pomalidomide(Non-covalent)

Y70.8: 11 residues within 4Å: Chain B: V.315, N.316, P.317, H.318, E.342, H.343, S.344, W.345, W.351, W.365, F.367 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.317, B:W.345, B:W.351, B:W.351, B:W.351, B:W.365, B:W.365, B:F.367 Hydrogen bonds: B:N.316, B:E.342, B:H.343, B:W.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bouguenina, H. et al., A Degron Blocking Strategy Towards Improved CRL4 CRBN Recruiting PROTAC Selectivity. Chembiochem (2023)

Release Date

2023-07-19

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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