SMTL ID : 6wwb.1

Crystal Structure of the second bromodomain of human BRD2 in complex with the compound 3b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Q.103, D.104, E.107, F.108 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.104, A:D.104 EDO.2: 5 residues within 4Å: Chain A: Y.28, D.94, A.97, M.98, K.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.101 EDO.3: 4 residues within 4Å: Chain A: L.10, K.11, N.14, M.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.11

1 x YA3: 2-((S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)-N-((1-(4-(2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)acetamido)butyl)-1H-1,2,3-triazol-4-yl)methyl)acetamide(Non-covalent)

YA3.4: 13 residues within 4Å: Chain A: W.30, P.31, F.32, V.36, L.41, L.43, C.85, Y.88, N.89, H.93, D.94, V.95, M.98 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.30, A:W.30, A:P.31, A:F.32, A:V.36, A:L.43, A:V.95, A:V.95 Hydrogen bonds: A:N.89, A:N.89, A:H.93 Water bridges: A:Y.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, J. et al., Phenyl-Glutarimides: Alternative Cereblon Binders for the Design of PROTACs. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2021-11-17

Peptides

Bromodomain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 2

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