SMTL ID : 7k6g.1 (1 other biounit)

Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-IN-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

3 x VYJ: 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one(Non-covalent)

VYJ.1: 8 residues within 4Å: Chain A: W.40, L.51, Y.98, N.99, D.103 Ligands: VYJ.2, VYJ.3, EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.51 Salt bridges: A:D.103 VYJ.2: 9 residues within 4Å: Chain A: Q.37, F.38, W.40, D.104, L.107, M.108 Ligands: VYJ.1, VYJ.3, EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.38, A:W.40, A:L.107 VYJ.3: 12 residues within 4Å: Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, Y.98, N.99, I.105 Ligands: VYJ.1, VYJ.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.40, A:P.41, A:L.51, A:L.53, A:L.53, A:Y.98, A:Y.98, A:I.105, A:I.105 Hydrogen bonds: A:N.99 Water bridges: A:Q.44, A:Q.44 pi-Stacking: A:W.40

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

EDO.4: 3 residues within 4Å: Chain A: W.40 Ligands: VYJ.1, VYJ.2 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62, A:T.62, A:N.94

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

2021-09-29

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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