7L9L: Second bromodomain (BD2) of human BRD3

Crystal structure of the second bromodomain (BD2) of human BRD3 bound to BI2536. Determined by X-ray diffraction at 1.55 Å resolution. Released 7 Jul 2021.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,213
Mol. weight: 13.89 kDa
Ligands: R78
Released: 7 Jul 2021

Explore 7L9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L9L contains 8 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	307-323	17
α-helix	325-327	3
α-helix	328-331	4
α-helix	332-334	3
α-helix	348-351	4
α-helix	358-366	9
α-helix	373-390	18
α-helix	396-413	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 3	A	protein	113	Homo sapiens	Q15059 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7L9L_1 Bromodomain-containing protein 3 (chains A)
SMGKLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKR
KMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP

Ligands and cofactors

ID	Name	Formula	Copies
R78	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]a…	C28 H39 N7 O3	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. Karim, R.M., Bikowitz, M.J., Chan, A. et al. J Med Chem (2021) 64:15772-15786. DOI 10.1021/acs.jmedchem.1c01096 · PubMed

Other PDB entries of the same protein (UniProt Q15059 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QJU 1.2 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with…
3S92 1.36 Å, Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor…
9NN4 1.37 Å, BET BRD3-BD1 in complex with peptide 7.2
2NXB 1.4 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3)
7TOA 1.41 Å, BRD3-BD1 in complex with RaPID linear peptide 3xAcK.1 (triAcK.1)
7LAY 1.45 Å, Crystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179
8CV5 1.47 Å, Peptide 4.2B in complex with BRD3.2
7L72 1.5 Å, Crystal structure of the second bromodomain (BD2) of human BRD3 bound to Ro3280
7RJL 1.5 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT
7TO8 1.5 Å, BRD3-BD1 in complex with RaPID linear peptide 2xAcK.1 (diAcK.1)
7TO9 1.6 Å, BRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE)
9MPN 1.6 Å, BRD3-BD1 A128T mutant

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