9GET | pdb_00009get

Crystal structure of CREBBP bromodomain in complex with (R,E)-6-(5-(7-methoxy-3,4-dihydroquinolin-1(2H)-yl)pent-1-en-1-yl)-4-methyl-8-(morpholine-4-carbonyl)-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one

PDB DOI: https://doi.org/10.2210/pdb9GET/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., Monoglu, M., Conway, S.
Funding Organization(s): German Research Foundation (DFG), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free:
0.167 (Depositor), 0.168 (DCC)
R-Value Work:
0.128 (Depositor), 0.142 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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)-6-(5-(7-methoxy-3,4-dihydroquinolin-1(2H)-yl)pent-1-en-1-yl)-4-methyl-8-(morpholine-4-carbonyl)-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one

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

To be published.

Macromolecule Content

Total Structure Weight: 14.74 kDa
Atom Count: 1,244
Modeled Residue Count: 119
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IKM (Subject of Investigation/LOI) Query on A1IKM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-8-morpholin-4-ylcarbonyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one C₃₀ H₃₈ N₄ O₄ YARRLUKCMVZYJK-HXRGIAOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.167 (Depositor), 0.168 (DCC)
R-Value Work: 0.128 (Depositor), 0.142 (DCC)
R-Value Observed: 0.130 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.038	α = 90
b = 34.773	β = 97.51
c = 91.268	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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 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.