7EIK | pdb_00007eik

RD4-BD1 in complex with LT-872-297

• PDB DOI: https://doi.org/10.2210/pdb7EIK/pdb

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


• Deposited: 2021-03-31 Released: 2022-04-06 
• Deposition Author(s): Zheng, W., Kong, B., Tang, W., Zhu, J., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

RD4-BD1 in complex with LT-872-297

Zheng, W., Kong, B., Tang, W., Zhu, J., Chen, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.3 kDa 
• Atom Count: 1,183 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	125	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J4R (Subject of Investigation/LOI)	B [auth A]	1-[2-methyl-5-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-4-(1-methylpyrazol-4-yl)-1H-pyrrol-3-yl]ethanone C23 H27 N7 O RWHIEFHJMQOKMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.82	α = 90
b = 47.34	β = 90
c = 82.51	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Zheng, W., Kong, B., Tang, W., Zhu, J., Chen, Y.

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description