7UGL | pdb_00007ugl

Bromodomain of CBP liganded with BMS-536924 and SGC-CBP30

• PDB DOI: https://doi.org/10.2210/pdb7UGL/pdb

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


• Deposited: 2022-03-24 Released: 2023-04-12 
• Deposition Author(s): Schonbrunn, E., Bikowitz, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structural basis of CBP and EP300 interaction with kinase inhibitors

Schonbrunn, E., Bikowitz, M.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.67 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 231 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase	A, B	116	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens) Explore Q92793  Go to UniProtKB:  Q92793
PHAROS:  Q92793 GTEx:  ENSG00000005339

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2LO (Subject of Investigation/LOI)	D [auth A], F [auth B]	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
N6I (Subject of Investigation/LOI)	C [auth A], E [auth B]	(3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one C25 H26 Cl N5 O3 ZWVZORIKUNOTCS-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2LO	BindingDB:  7UGL	Kd: min: 21, max: 35 (nM) from 4 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: 1.50 Å
• R-Value Free:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.08	α = 90
b = 59.49	β = 109.76
c = 57.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Schonbrunn, E., Bikowitz, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description