5BT3

Crystal structure of EP300 bromodomain in complex with SGC-CBP30 chemical probe

• PDB DOI: https://doi.org/10.2210/pdb5BT3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-02 Released: 2015-07-01 
• Deposition Author(s): Tallant, C., Hay, D., Krojer, T., Nunez-Alonso, G., Picaud, S., Newman, J.A., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.178 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Crystal structure of EP300 bromodomain in complex with a 3,5-dimethylisoxazol ligand

Tallant, C., Hay, D., Krojer, T., Nunez-Alonso, G., Picaud, S., Newman, J.A., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.4 kDa 
• Atom Count: 1,205 
• Modelled Residue Count: 114 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A	116	Homo sapiens	Mutation(s): 0  Gene Names: EP300, P300 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens) Explore Q09472  Go to UniProtKB:  Q09472
GTEx:  ENSG00000100393

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2LO	B [auth A]	2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole C28 H33 Cl N4 O3 GEPYBHCJBORHCE-SFHVURJKSA-N
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2LO	BindingDB:  5BT3	Kd: min: 21, max: 32 (nM) from 2 assay(s)
		IC50: min: 30, max: 2800 (nM) from 10 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.178 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.431	α = 90
b = 53.431	β = 90
c = 77.003	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Tallant, C., Hay, D., Krojer, T., Nunez-Alonso, G., Picaud, S., Newman, J.A., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description