9GEW | pdb_00009gew

Crystal structure of CREBBP bromodomain in complex with (R,E)-6-(5-(6-methoxy-2,3-dihydro-4H-benzo[b][1,4]oxazin-4-yl)pent-1-en-1-yl)-4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one

• PDB DOI: https://doi.org/10.2210/pdb9GEW/pdb

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


• Deposited: 2024-08-07 Released: 2025-08-20 
• Deposition Author(s): Amann, M., Boyd, A., Einsle, O., Moroglu, M., Conway, S.
• Funding Organization(s): German Research Foundation (DFG), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CREBBP bromodomain in complex with (R,E)-6-(5-(6-methoxy-2,3-dihydro-4H-benzo[b][1,4]oxazin-4-yl)pent-1-en-1-yl)-4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one

Amann, M., Boyd, A., Einsle, O., Moroglu, M., Conway, S.

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

Macromolecule Content 

• Total Structure Weight: 14.9 kDa 
• Atom Count: 1,309 
• Modeled Residue Count: 119 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREBBP	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IKI (Subject of Investigation/LOI)	B [auth A]	(4~{R})-6-[(~{E})-5-(6-methoxy-2,3-dihydro-1,4-benzoxazin-4-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one C24 H29 N3 O3 GEUPZGDPLUFWOK-QGZVFWFLSA-N
BU3	C [auth A], D [auth A], E [auth A]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.468	α = 90
b = 49.147	β = 90
c = 79.766	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Amann, M., Boyd, A., Einsle, O., Moroglu, M., Conway, S.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	RTG2202
Other government		DMT00011

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release