6QJU

Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with 3-bromo-1H-indazol-5-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Br-O-modomain (BRD3) halogen binding to a small molecule

Braun, M.B.Stehle, S.Heidrich, J.Boeckler, F.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 3
A, B
123Homo sapiensMutation(s): 0 
Gene Names: BRD3KIAA0043RING3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q15059 (Homo sapiens)
Explore Q15059 
Go to UniProtKB:  Q15059
PHAROS:  Q15059
GTEx:  ENSG00000169925 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15059
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J58 (Subject of Investigation/LOI)
Query on J58

Download Ideal Coordinates CCD File 
F [auth A]3-bromanyl-2~{H}-indazol-5-amine
C7 H6 Br N3
AOKHRTSXJINPPJ-UHFFFAOYSA-N
DMS
Query on DMS

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H [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
E [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.951α = 90
b = 62.071β = 90
c = 84.783γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description