6U0D

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZL0590

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

Discovery, X-ray Crystallography, and Anti-inflammatory Activity of Bromodomain-containing Protein 4 (BRD4) BD1 Inhibitors Targeting a Distinct New Binding Site

Liu, Z., Li, Y., Chen, H., Lai, H., Wang, P., Wu, S., Wold, E.A., Leonard, P.G., Joseph, S., Hu, H., Chiang, C., Brasier, A.R., Tian, B., Zhou, J.

(2022) J Med Chem 


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POJ (Subject of Investigation/LOI)
Query on POJ
Download Ideal Coordinates CCD File 
C [auth A]N-[4-({(2S)-2-[(morpholin-4-yl)methyl]pyrrolidin-1-yl}sulfonyl)phenyl]-N'-[4-(trifluoromethyl)phenyl]urea
C23 H27 F3 N4 O4 S
ZPMULUKHFNMJPF-FQEVSTJZSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
POJ BindingDB:  6U0D IC50: min: 90, max: 1093 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.47α = 90
b = 42.38β = 90
c = 80.29γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Crohns and Colitis FoundationUnited States576144

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 2.0: 2022-01-19
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Refinement description