6K04: BRD2(BD2)with ligand BY27 bound

Crystal structure of BRD2(BD2)with ligand BY27 bound. Determined by X-ray diffraction at 1.25 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,068
Mol. weight: 13.56 kDa
Ligands: CQF
Released: 18 Sept 2019

Explore 6K04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K04 contains 9 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: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	348-360	13
α-helix	363-365	3
α-helix	366-369	4
α-helix	370-372	3
α-helix	378-381	4
α-helix	386-389	4
α-helix	396-404	9
α-helix	411-428	18
α-helix	434-450	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 2	A	protein	112	Homo sapiens	P25440 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6K04_1 Bromodomain-containing protein 2 (chains A)
GKLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKM
ENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD

Ligands and cofactors

ID	Name	Formula	Copies
CQF	(6~{R})-~{N}-(4-chlorophenyl)-1-methyl-8-(1-methylpyrazol-4-yl)-5,6-dihydro-4~{…	C22 H21 Cl N6	1

Primary citation

Discovery, structural insight, and bioactivities of BY27 as a selective inhibitor of the second bromodomains of BET proteins. Chen, D., Lu, T., Yan, Z. et al. Eur J Med Chem (2019) 182:111633-111633. DOI 10.1016/j.ejmech.2019.111633 · PubMed

Other PDB entries of the same protein (UniProt P25440 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IG6 0.91 Å, Ultra-high resolution crystal structure of second bromodomain of BRD2 in complex with…
5IBN 0.94 Å, Ultra high resolution crystal structure of the apo- form of second bromodomain of BRD2.
6DBC 1.05 Å, Second bromodomain of Human BRD2 with a Tetrahydroquinoline analogue
6DDJ 1.05 Å, Crystal Structure of the human BRD2 BD2 bromodimain in complex with a…
4J1P 1.08 Å, X-ray crystal structure of bromodomain 2 of human brd2 in complex with rvx208 to 1.08 A…
7VRM 1.1 Å, crystal structure of BRD2-BD2 in complex with purine derivative
6I80 1.14 Å, Crystal Structure of the second bromodomain of BRD2 in complex with RT53
7VRQ 1.15 Å, crystal structure of BRD2-BD2 in complex with purine derivative
24KK 1.2 Å, Crystal structure of the second bromodomain (BD2) of human BRD2 in complex with…
5O38 1.2 Å, Human Brd2(BD2) mutant in free form
5O3I 1.2 Å, Human Brd2(BD2) mutant in complex with AL-tBu
7USG 1.2 Å, BRD2-BD2 in complex with MDP5

Browse structure collections

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