6ZEL | pdb_00006zel

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5

PDB DOI: https://doi.org/10.2210/pdb6ZEL/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-16 Released: 2020-07-29
Deposition Author(s): Krojer, T., Martinez-Cartro, M., Picaud, S., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Barril, X., von Delft, F.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free:
0.147 (Depositor), 0.140 (DCC)
R-Value Work:
0.125 (Depositor), 0.130 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5

Martinez-Cartro, M., Barril, X.

To be published.

Macromolecule Content

Total Structure Weight: 15.52 kDa
Atom Count: 1,303
Modeled Residue Count: 126
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A [auth AAA]	127	Homo sapiens	Mutation(s): 0 Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885 Go to UniProtKB: O60885
PHAROS: O60885 GTEx: ENSG00000141867
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QGQ (Subject of Investigation/LOI) Query on QGQ Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA]	3,5-dimethyl-4-[(6-methylpyrimidin-4-yl)sulfanylmethyl]-1,2-oxazole C₁₁ H₁₃ N₃ O S ROKHJFVYDKKVDA-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain B [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA]	B [auth AAA], C [auth AAA], D [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA]

Binding Affinity Annotations
ID	Source	Binding Affinity
QGQ	BindingDB: 6ZEL	IC50: 3.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.147 (Depositor), 0.140 (DCC)
R-Value Work: 0.125 (Depositor), 0.130 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.235	α = 90
b = 44.141	β = 90
c = 78.441	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2021-05-19
Changes: Experimental preparation
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description