4LZS | pdb_00004lzs

Crystal Structure of BRD4(1) bound to inhibitor XD46

PDB DOI: https://doi.org/10.2210/pdb4LZS/pdb

Classification: PROTEIN BINDING/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-01 Released: 2014-01-15
Deposition Author(s): Wohlwend, D., Huegle, M., Einsle, O., Gerhardt, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.192 (Depositor), 0.198 (DCC)
R-Value Observed:
0.195 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

4-Acyl pyrroles: mimicking acetylated lysines in histone code reading.

Lucas, X., Wohlwend, D., Hugle, M., Schmidtkunz, K., Gerhardt, S., Schule, R., Jung, M., Einsle, O., Gunther, S.

(2013) Angew Chem Int Ed Engl 52: 14055-14059

PubMed: 24272870 Search on PubMed
DOI: https://doi.org/10.1002/anie.201307652
Primary Citation Related Structures:
4LYI, 4LYS, 4LYW, 4LZR, 4LZS

Organizational Affiliation

Pharmazeutische Bioinformatik, Institut für Pharmazeutische, Wissenschaften, Albert-Ludwigs-Universität, Hermann-Herder-Strasse 9, 79104 Freiburg (Germany) http://www.pharmaceutical-bioinformatics.org.

Macromolecule Content

Total Structure Weight: 15.31 kDa
Atom Count: 1,184
Modeled Residue Count: 127
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
L46 Query on L46 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-acetyl-3-ethyl-N,5-dimethyl-1H-pyrrole-2-carboxamide C₁₁ H₁₆ N₂ O₂ LCSLEHAEHBSCSA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
L46	BindingDB: 4LZS	Kd: min: 6800, max: 2.40e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.192 (Depositor), 0.198 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.42	α = 90
b = 43.9	β = 90
c = 77.53	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.