4NR4 | pdb_00004nr4

Crystal structure of the bromodomain of human CREBBP in complex with an isoxazolyl-benzimidazole ligand

• PDB DOI: https://doi.org/10.2210/pdb4NR4/pdb

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


• Deposited: 2013-11-26 Released: 2013-12-18 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Hay, D., Fedorov, O., Martin, S., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human CREBBP in complex with an isoxazolyl-benzimidazole ligand

Filippakopoulos, P., Picaud, S., Felletar, I., Hay, D., Fedorov, O., Martin, S., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., 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)

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: 29.61 kDa 
• Atom Count: 2,241 
• Modelled Residue Count: 225 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A, B	119	Homo sapiens	Mutation(s): 0  Gene Names: CBP, 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2LK	C [auth A], E [auth B], F [auth B]	1-(4-chlorobenzyl)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-benzimidazole C19 H16 Cl N3 O WPKUYRYYDUHEAQ-UHFFFAOYSA-N
EDO	D [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.87	α = 90
b = 57.11	β = 90
c = 82.84	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Hay, D., Fedorov, O., Martin, S., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description