Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 16.50 kDa 
• Atom Count: 1281 
• Modelled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

6HKR

Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC271.

• PDB DOI: 10.2210/pdb6HKR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-09-07 Released: 2018-11-28 
• Deposition Author(s): Tomlinson, C., Chisholm, D., Whiting, A., Pohl, E.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.175 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Literature

Novel Fluorescence Competition Assay for Retinoic Acid Binding Proteins.

Tomlinson, C.W.E., Chisholm, D.R., Valentine, R., Whiting, A., Pohl, E.

(2018) ACS Med Chem Lett 9: 1297-1300

• PubMed: 30613343 
• DOI: 10.1021/acsmedchemlett.8b00420
• Primary Citation of Related Structures:  
  6HKR


• PubMed Abstract: 
  

Vitamin A derived retinoid compounds have multiple, powerful roles in the cellular growth and development cycle and, as a result, have attracted significant attention from both academic and pharmaceutical research in developing and characterizing synthetic retinoid analogues. Simplifying the hit development workflow for retinoid signaling will improve options available for tackling related pathologies, including tumor growth and neurodegeneration. Here, we present a novel assay that employs an intrinsically fluorescent synthetic retinoid, DC271, which allows direct measurement of the binding of nonlabeled compounds to relevant proteins. The method allows for straightforward initial measurement of binding using existing compound libraries and is followed by calculation of binding constants using a dilution series of plausible hits. The ease of use, high throughput format, and measurement of both qualitative and quantitative binding offer a new direction for retinoid-related pharmacological development.

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Organizational Affiliation: 

Department of Biosciences, Durham University, Science Laboratories, South Road, Durham, DH1 3LE, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular retinoic acid-binding protein 2	A	138	Homo sapiens	Mutation(s): 0  Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens) Explore P29373  Go to UniProtKB:  P29373
PHAROS:  P29373

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G9Q (Subject of Investigation/LOI)	C [auth A]	4-[2-(4,4-dimethyl-1-propan-2-yl-2,3-dihydroquinolin-6-yl)ethynyl]benzoic acid C23 H25 N O2 OCMSZODRCJAGHL-UHFFFAOYSA-N
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.175 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.689	α = 90
b = 47.479	β = 90
c = 77.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-09-07 
• Released Date: 2018-11-28 
Deposition Author(s): Tomlinson, C., Chisholm, D., Whiting, A., Pohl, E.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references