SMTL ID : 7l6d.1

Crystal structure of the second bromodomain (BD2) of human BRD2 bound to bromosporine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x BMF: Bromosporine(Non-covalent)

BMF.1: 14 residues within 4Å: Chain A: W.29, P.30, F.31, K.33, P.34, V.35, D.36, L.40, L.42, C.84, N.88, H.92, V.94 Ligands: EDO.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.29, A:W.29, A:F.31, A:V.35, A:L.40, A:L.40, A:L.42 Hydrogen bonds: A:D.36, A:N.88, A:N.88

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

EDO.2: 1 residues within 4Å: Ligands: EDO.4 No protein-ligand interaction detected (PLIP) EDO.3: 7 residues within 4Å: Chain A: I.48, I.49, K.50, H.51, L.79, N.83, K.86 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.50, A:H.51, A:H.51, A:N.83, A:K.86, A:K.86 EDO.4: 5 residues within 4Å: Chain A: P.34, T.57, R.60 Ligands: EDO.2, EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.57, A:R.60 Water bridges: A:R.60 EDO.5: 4 residues within 4Å: Chain A: H.46, I.49, K.50, P.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.46 EDO.6: 5 residues within 4Å: Chain A: P.34, P.52, T.57, R.60 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.57, A:R.60 EDO.7: 2 residues within 4Å: Chain A: D.36 Ligands: BMF.1 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: S.21, K.22, K.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.22, A:K.22, A:K.23 EDO.9: 2 residues within 4Å: Chain A: H.46, D.47 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: N.13, E.63, R.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.13 Water bridges: A:K.17, A:R.65 Salt bridges: A:R.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karim, R.M. et al., Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. J.Med.Chem. (2021)

Release Date

2021-06-23

Peptides

Bromodomain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 2

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