6YIL | pdb_00006yil

Crystal structure of the CREBBP bromodomain in complex with a tetrahydroquinoxaline ligand

PDB DOI: https://doi.org/10.2210/pdb6YIL/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free:
0.151 (Depositor), 0.197 (DCC)
R-Value Work:
0.132 (Depositor)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of the CREBBP bromodomain in complex with a tetrahydroquinoxaline 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.

Macromolecule Content

Total Structure Weight: 14.64 kDa
Atom Count: 1,160
Modeled Residue Count: 113
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OSQ (Subject of Investigation/LOI) Query on OSQ 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]	(3~{R})-~{N}-[3-(3,4-dihydro-2~{H}-quinolin-1-yl)-2,2-bis(fluoranyl)propyl]-3-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinoxaline-5-carboxamide C₂₂ H₂₄ F₂ N₄ O₂ HTEQIZSWLJNYLH-CQSZACIVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.151 (Depositor), 0.197 (DCC)
R-Value Work: 0.132 (Depositor)
R-Value Observed: 0.133 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.26	α = 90
b = 34.62	β = 107.29
c = 40.11	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Arrowsmith, C.H.

Filippakopoulos, P.

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

Revision History (Full details and data files)

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

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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.