7RUW | pdb_00007ruw

Crystal structure of the BCL6 BTB domain in complex with OICR-7859

• PDB DOI: https://doi.org/10.2210/pdb7RUW/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-08-18 Released: 2022-11-09 
• Deposition Author(s): Kuntz, D.A., Prive, G.G.
• Funding Organization(s): Ontario Institute for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.169 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.140 (Depositor) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the BCL6 BTB domain in complex with OICR-7859

Mamai, A., Isaac, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 15.05 kDa 
• Atom Count: 1,160 
• Modeled Residue Count: 122 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	127	Homo sapiens	Mutation(s): 3  Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens) Explore P41182  Go to UniProtKB:  P41182
PHAROS:  P41182 GTEx:  ENSG00000113916

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7RR (Subject of Investigation/LOI)	B [auth A]	2-(2-amino-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-N-(3-chloropyridin-4-yl)acetamide C13 H11 Cl N6 O2 MOOOFDHGGWGWDP-UHFFFAOYSA-N
FMT	C [auth A], D [auth A], E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
7RR	BindingDB:  7RUW	Kd: min: 1.00e+4, max: 1.10e+4 (nM) from 2 assay(s)
		IC50: 1.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.169 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.140 (Depositor) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.33	α = 90
b = 72.133	β = 107.14
c = 55.493	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Kuntz, D.A., Prive, G.G.

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Funding Organization	Location	Grant Number
Ontario Institute for Cancer Research		--

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description