5DKD

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe

Tallant, C.Owen, D.R.Gerstenberger, B.S.Fedorov, O.Savitsky, P.Nunez-Alonso, G.Newman, J.A.Filippakopoulos, P.Burgess-Brown, N.von Delft, F.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Muller, S.Knapp, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription activator BRG1
A, B
121Homo sapiensMutation(s): 0 
Gene Names: SMARCA4BAF190ABRG1SNF2BSNF2L4
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51532 (Homo sapiens)
Explore P51532 
Go to UniProtKB:  P51532
PHAROS:  P51532
GTEx:  ENSG00000127616 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51532
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5BW
Query on 5BW

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one
C19 H19 N3 O2
INAICWLVUAKEPB-QSTFCLMHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
I [auth B]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5BW BindingDB:  5DKD Kd: min: 21, max: 100 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.926α = 90
b = 74.566β = 109.9
c = 52.626γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description