7L72: Second bromodomain (BD2) of human BRD3

Crystal structure of the second bromodomain (BD2) of human BRD3 bound to Ro3280. Determined by X-ray diffraction at 1.5 Å resolution. Released 17 Nov 2021.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,207
Mol. weight: 13.85 kDa
Ligands: 79C
Released: 17 Nov 2021

Explore 7L72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L72 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

>7L72_1 Bromodomain-containing protein 3 (chains A)
SMGKLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKR
KMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP

Ligands and cofactors

ID	Name	Formula	Copies
79C	4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,…	C27 H35 F2 N7 O3	1

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
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)
7L9L 1.55 Å, Crystal structure of the second bromodomain (BD2) of human BRD3 bound to BI2536
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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