SMTL ID : 6bn7.1

Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.344, C.347, C.412, C.415 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.344, B:C.347, B:C.412, B:C.415

1 x RN3: methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate(Non-covalent)

RN3.2: 21 residues within 4Å: Chain B: N.372, P.373, H.374, E.398, H.399, S.400, W.401, W.407, W.421, F.423 Chain C: W.40, P.41, F.42, Q.43, Q.44, V.46, L.53, Y.56, Y.98, N.99, I.105 23 PLIP interactions: 15 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:W.40, C:W.40, C:W.40, C:W.40, C:F.42, C:V.46, C:L.53, C:Y.98, C:I.105, C:I.105, B:W.401, B:W.407, B:F.423 Hydrogen bonds: C:Q.44, C:Y.56, C:N.99, B:N.372, B:S.396, B:H.399, B:W.401, B:F.402 pi-Stacking: C:W.40, C:W.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R.P. et al., Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat. Chem. Biol. (2018)

Release Date

2018-05-30

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B
Bromodomain-containing protein 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Bromodomain-containing protein 4

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