5BT3

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

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
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This is version 1.1 of the entry. See complete history. 


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.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase p300116Homo sapiensMutation(s): 0 
Gene Names: EP300, P300
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
PHAROS:  Q09472
GTEx:  ENSG00000100393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09472
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2LO
Query on 2LO
Download Ideal Coordinates CCD File 
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
Query on IPA
Download Ideal Coordinates CCD File 
C [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2LO BindingDB:  5BT3 Kd: min: 21, max: 32 (nM) from 3 assay(s)
IC50: min: 28, max: 2800 (nM) from 12 assay(s)
EC50: 6900 (nM) from 1 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 = 53.431α = 90
b = 53.431β = 90
c = 77.003γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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