5DKH

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl propenone inhibitor 17

• PDB DOI: https://doi.org/10.2210/pdb5DKH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-03 Released: 2016-09-14 
• Deposition Author(s): Tallant, C., Owen, D.R., Taylor, A., Fedorov, O., Savitsky, P., Siejka, P., Srikannathasan, V., Nowak, R., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl propenone inhibitor 17

Tallant, C., Owen, D.R., Taylor, A., Fedorov, O., Savitsky, P., Siejka, P., Srikannathasan, V., Nowak, R., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.38 kDa 
• Atom Count: 3,037 
• Modelled Residue Count: 339 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable global transcription activator SNF2L2	A, B, C	123	Homo sapiens	Mutation(s): 0  Gene Names: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens) Explore P51531  Go to UniProtKB:  P51531
PHAROS:  P51531 GTEx:  ENSG00000080503

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5C0	F [auth A], K [auth B]	(2E)-3-[(6S,9R)-4-(cyclopropylamino)-6,7,8,9-tetrahydro-5H-6,9-epiminocyclohepta[d]pyrimidin-10-yl]-1-(2-hydroxyphenyl)prop-2-en-1-one C21 H22 N4 O2 RQOKOKQQGKYASH-FPBOJHQQSA-N
ZN	D [auth A], E [auth A], G [auth B], H [auth B], L [auth C], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5C0	BindingDB:  5DKH	Kd: 37 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.241 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.997	α = 90
b = 63.997	β = 90
c = 89.16	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Tallant, C., Owen, D.R., Taylor, A., Fedorov, O., Savitsky, P., Siejka, P., Srikannathasan, V., Nowak, R., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description