9GEY | pdb_00009gey

Crystal structure of CREBBP bromodomain in complex with (R,E)-2-methyl-1,2,3,5,9,10,11,12,18,19,22,23-dodecahydro-17H,21H-14,16-etheno-7,26-(metheno)[1,4]diazepino[2,3-l]pyrido[2,1-d][1]oxa[5,17]diazacycloicosine-4,8-dione

PDB DOI: https://doi.org/10.2210/pdb9GEY/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., Guenther, S., Moroglu, M., Conway, S.
Funding Organization(s): German Research Foundation (DFG), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9GEY

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of CREBBP bromodomain in complex with (R,E)-2-methyl-1,2,3,5,9,10,11,12,18,19,22,23-dodecahydro-17H,21H-14,16-etheno-7,26-(metheno)[1,4]diazepino[2,3-l]pyrido[2,1-d][1]oxa[5,17]diazacycloicosine-4,8-dione

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

To be published.

Macromolecule Content

Total Structure Weight: 29.46 kDa
Atom Count: 2,460
Modeled Residue Count: 231
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREBBP	A, B	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IKK (Subject of Investigation/LOI) Query on A1IKK Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	(R,E)-2-methyl-1,2,3,5,9,10,11,12,18,19,22,23-dodecahydro-17H,21H-14,16-etheno-7,26-(metheno)[1,4]diazepino[2,3-l]pyrido[2,1-d][1]oxa[5,17]diazacycloicosine-4,8-dione C₂₈ H₃₆ N₄ O₃ LWYJFDNVCBLIQC-LJQANCHMSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.211 (Depositor), 0.212 (DCC)
R-Value Work: 0.171 (Depositor), 0.171 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.363	α = 98.09
b = 45.273	β = 105.54
c = 50.073	γ = 90.05

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.