7R8R: Physachenolide C with Bromodomain

Physachenolide C with Bromodomain (BRD3-BD1). Determined by X-ray diffraction at 1.8 Å resolution. Released 21 Sept 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,055
Mol. weight: 14.92 kDa
Ligands: 8L6
Released: 21 Sept 2022

Explore 7R8R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R8R 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	37-41	5
α-helix	42-47	6
α-helix	48-51	4
α-helix	57-59	3
α-helix	73-76	4
α-helix	83-91	9
α-helix	98-115	18
α-helix	121-138	18
α-helix	141-143	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 3	A	protein	121	Homo sapiens	Q15059 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7R8R_1 Bromodomain-containing protein 3 (chains A)
PEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDM
GTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQE
E

Ligands and cofactors

ID	Name	Formula	Copies
8L6	Physachenolide C	C30 H42 O9	1

Primary citation

Physachenolide C is a Potent, Selective BET Inhibitor. Zerio, C.J., Sivinski, J., Wijeratne, E.M.K. et al. J Med Chem (2023) 66:913-933. DOI 10.1021/acs.jmedchem.2c01770 · 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)
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)

Browse structure collections

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