6YIJ

Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand

• PDB DOI: https://doi.org/10.2210/pdb6YIJ/pdb

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


• Deposited: 2020-04-01 Released: 2020-04-15 
• Deposition Author(s): Picaud, S., Brand, M., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Conway, S., Filippakopoulos, P.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand

Picaud, S., Brand, M., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Conway, S., Filippakopoulos, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.4 kDa 
• Atom Count: 7,177 
• Modelled Residue Count: 813 
• Deposited Residue Count: 833 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREBBP	A, B, C, D, E, F, G	119	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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
OSN (Subject of Investigation/LOI)	H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G]	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one C25 H31 N3 O2 VBTDHMQUNCGCSZ-SBLNNXNXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OSN	BindingDB:  6YIJ	Kd: min: 100, max: 240 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.694	α = 90
b = 96.694	β = 90
c = 251.713	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Picaud, S., Brand, M., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Conway, S., Filippakopoulos, P.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N010051/1

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description