5LPM: Bromodomain of human Ep300

Crystal structure of the bromodomain of human Ep300 bound to the inhibitor XDM3d. Determined by X-ray diffraction at 1.5 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,465
Mol. weight: 29.33 kDa
Ligands: 71Y
Released: 16 Aug 2017

Explore 5LPM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LPM contains 12 α-helices and 0 β-strands across 2 chains. 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	1051-1066	16
α-helix	1073-1075	3
α-helix	1089-1092	4
α-helix	1099-1108	10
α-helix	1114-1131	18
α-helix	1137-1160	24

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	1051-1066	16
α-helix	1073-1075	3
α-helix	1089-1092	4
α-helix	1099-1107	9
α-helix	1114-1131	18
α-helix	1137-1160	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone acetyltransferase p300	A, B	protein	116	Homo sapiens	Q09472 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5LPM_1 Histone acetyltransferase p300 (chains A, B)
SMIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRK
LDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLG

Ligands and cofactors

ID	Name	Formula	Copies
71Y	~{N}-[(1~{S},2~{S})-7-chloranyl-2-oxidanyl-1,2,3,4-tetrahydronaphthalen-1-yl]-4…	C20 H23 Cl N2 O3	4

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

Primary citation

Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles. Hugle, M., Lucas, X., Ostrovskyi, D. et al. Angew Chem Int Ed Engl (2017) 56:12476-12480. DOI 10.1002/anie.201705516 · PubMed

Other PDB entries of the same protein (UniProt Q09472 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BT3 1.05 Å, Crystal structure of EP300 bromodomain in complex with SGC-CBP30 chemical probe
3T92 1.5 Å, Crystal structure of the Taz2:C/EBPepsilon-TAD chimera protein
5NU5 1.6 Å, Crystal structure of the human bromodomain of EP300 bound to the inhibitor XDM-CBP
3BIY 1.7 Å, Crystal structure of p300 histone acetyltransferase domain in complex with a bisubstrate…
6PGU 1.72 Å, Crystal structure of the p300 acetyltransferase domain with allosteric inhibitor CPI-076…
6V8K 1.84 Å, Crystal structure of the p300 acetyltransferase domain with peptide-competitive…
4PZS 1.94 Å, Crystal structure of p300 histone acetyltransferase domain in complex with…
5KJ2 1.95 Å, The novel p300/CBP inhibitor A-485 uncovers a unique mechanism of action to target AR in…
6DS6 1.95 Å, Crystal structure of p300 ZZ domain in complex with histone H3 peptide
7QGS 2.0 Å, Crystal structure of p300 CH1 domain in complex with CITIF (a CITED2-HIF-1alpha hybrid)
7UGI 2.0 Å, Bromodomain of EP300 liganded with BMS-536924
7VHZ 2.0 Å, Crystal structure of EP300 HAT domain in complex with compound 7

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