Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.65 kDa 
• Atom Count: 1032 
• Modelled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

2D82

Target Structure-Based Discovery of Small Molecules that Block Human p53 and CREB Binding Protein (CBP) Association

• PDB DOI: 10.2210/pdb2D82/pdb
• BMRB: 6960

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


• Deposited: 2005-12-01 Released: 2006-04-04 
• Deposition Author(s): Sachchidanand, Resnick-Silverman, L., Yan, S., Mujtaba, S., Liu, W.J., Zeng, L., Manfredi, J.J., Zhou, M.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 1 
• Selection Criteria: structures with the least restraint violations 

Literature

Target structure-based discovery of small molecules that block human p53 and CREB binding protein association

Sachchidanand, Resnick-Silverman, L., Yan, S., Mutjaba, S., Liu, W.J., Zeng, L., Manfredi, J.J., Zhou, M.M.

(2006) Chem Biol 13: 81-90

• PubMed: 16426974 
• DOI: 10.1016/j.chembiol.2005.10.014
• Primary Citation of Related Structures:  
  2D82


• PubMed Abstract: 
  

Lysine acetylation of human tumor suppressor p53 in response to cellular stress signals is required for its function as a transcription factor that regulates cell cycle arrest, senescence, or apoptosis. Here, we report small molecules that block lysine 382-acetylated p53 association with the bromodomain of the coactivator CBP, an interaction essential for p53-induced transcription of the cell cycle inhibitor p21 in response to DNA damage. These chemicals were discovered in target structure-guided nuclear magnetic resonance spectroscopy screening of a focused chemical library constructed based on the structural knowledge of CBP bromodomain/p53-AcK382 binding. Structural characterization shows that these chemicals inhibit CBP/p53 association by binding to the acetyl-lysine binding site of the bromodomain. Cell-based functional assays demonstrate that the lead chemicals can modulate p53 stability and function in response to DNA damage.

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Organizational Affiliation: 

Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York 10029, USA.

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTR	B [auth A]	9-ACETYL-2,3,4,9-TETRAHYDRO-1H-CARBAZOL-1-ONE C14 H13 N O2 MIGJEXKBUJPKJF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TTR	BindingDB:  2D82	Kd: 1.96e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 1 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2D82 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-01 
• Released Date: 2006-04-04 
Deposition Author(s): Sachchidanand, Resnick-Silverman, L., Yan, S., Mujtaba, S., Liu, W.J., Zeng, L., Manfredi, J.J., Zhou, M.M.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations