2L84 | pdb_00002l84

Solution NMR structures of CBP bromodomain with small molecule j28

• PDB DOI: https://doi.org/10.2210/pdb2L84/pdb
• BMRB: 17392

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 1520
• Mutation(s): No 


• Deposited: 2011-01-03 Released: 2011-01-19 
• Deposition Author(s): Borah, J.C., Mujtaba, S., Karakikes, I., Zeng, L., Muller, M., Patel, J., Moshkina, N., Morohashi, K., Zhang, W., Gerona-Navarro, G., Hajjar, R.J., Zhou, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

A Small Molecule Binding to the Coactivator CREB-Binding Protein Blocks Apoptosis in Cardiomyocytes.

Borah, J.C., Mujtaba, S., Karakikes, I., Zeng, L., Muller, M., Patel, J., Moshkina, N., Morohashi, K., Zhang, W., Gerona-Navarro, G., Hajjar, R.J., Zhou, M.M.

(2011) Chem Biol 18: 531-541

• PubMed: 21513889 
• DOI: https://doi.org/10.1016/j.chembiol.2010.12.021
• Primary Citation Related Structures: 
  2L84, 2L85


• PubMed Abstract: 
  

  As a master transcription factor in cellular responses to external stress, tumor suppressor p53 is tightly regulated. Excessive p53 activity during myocardial ischemia causes irreversible cellular injury and cardiomyocyte death. p53 activation is dependent on lysine acetylation by the lysine acetyltransferase and transcriptional coactivator CREB-binding protein (CBP) and on acetylation-directed CBP recruitment for p53 target gene expression. Here, we report a small molecule ischemin, developed with a structure-guided approach to inhibit the acetyl-lysine binding activity of the bromodomain of CBP. We show that ischemin alters post-translational modifications on p53 and histones, inhibits p53 interaction with CBP and transcriptional activity in cells, and prevents apoptosis in ischemic cardiomyocytes. Our study suggests small molecule modulation of acetylation-mediated interactions in gene transcription as a new approach to therapeutic interventions of human disorders such as myocardial ischemia.

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Organizational Affiliation: 
• Department of Structural and Chemical Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.75 kDa 
• Atom Count: 1,038 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	121	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP, CBP 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J28	B [auth A]	5-[(E)-(2-amino-4-hydroxy-5-methylphenyl)diazenyl]-2,4-dimethylbenzenesulfonic acid C15 H17 N3 O4 S UUECJWRVDTUDCB-ISLYRVAYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J28	BindingDB:  2L84	Kd: min: 1.90e+4, max: 1.96e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Borah, J.C., Mujtaba, S., Karakikes, I., Zeng, L., Muller, M., Patel, J., Moshkina, N., Morohashi, K., Zhang, W., Gerona-Navarro, G., Hajjar, R.J., Zhou, M.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations