3SVF | pdb_00003svf

Crystal Structure of the first bromodomain of human BRD4 in complex with a dihydro-quinazolin ligand

PDB DOI: https://doi.org/10.2210/pdb3SVF/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-12 Released: 2011-08-10
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.227 (Depositor), 0.235 (DCC)
R-Value Work:
0.177 (Depositor), 0.182 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the first bromodomain of human BRD4 in complex with a dihydro-quinazolin ligand

Filippakopoulos, P., Picaud, S., Felletar, I., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 15.42 kDa
Atom Count: 1,163
Modeled Residue Count: 127
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WDR Query on WDR 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]	(4S)-6-(3,5-dimethyl-1,2-oxazol-4-yl)-4-(2-hydroxyethoxy)-3-methyl-3,4-dihydroquinazolin-2(1H)-one C₁₆ H₁₉ N₃ O₄ PRJSSNHOEZPGMA-HNNXBMFYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.227 (Depositor), 0.235 (DCC)
R-Value Work: 0.177 (Depositor), 0.182 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.56	α = 90
b = 48.98	β = 90
c = 60.28	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description