4WHW | pdb_00004whw

Direct photocapture of bromodomains using tropolone chemical probes

• PDB DOI: https://doi.org/10.2210/pdb4WHW/pdb

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


• Deposited: 2014-09-23 Released: 2015-10-28 
• Deposition Author(s): Hett, E.C., Piatnitski Chekler, E.L., Basak, A., Bonin, P.D., Denny, R.A., Flick, A.C., Geoghegan, K.F., Liu, S., Pletcher, M.T., Robinson, R.P., Sahasrabudhe, P., Salter, S., Stock, I.A., Jones, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Direct photocapture of bromodomains using tropolone chemical probes

Hett, E.C., Piatnitski Chekler, E.L., Basak, A., Bonin, P.D., Denny, R.A., Flick, A.C., Geoghegan, K.F., Liu, S., Pletcher, M.T., Robinson, R.P., Sahasrabudhe, P., Salter, S., Stock, I.A., Jones, L.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.63 kDa 
• Atom Count: 1,197 
• Modeled Residue Count: 124 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3OT	B [auth A]	2-methoxy-4-{1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazol-5-yl}cyclohepta-2,4,6-trien-1-one C29 H31 N3 O3 ZSTNBLSPAMZIQD-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3OT	BindingDB:  4WHW	IC50: 350 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.83	α = 90
b = 50.591	β = 90
c = 57.468	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Hett, E.C., Piatnitski Chekler, E.L., Basak, A., Bonin, P.D., Denny, R.A., Flick, A.C., Geoghegan, K.F., Liu, S., Pletcher, M.T., Robinson, R.P., Sahasrabudhe, P., Salter, S., Stock, I.A., Jones, L.H.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations