6HKR | pdb_00006hkr

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6HKR

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00420
  • Primary Citation 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.


  • Organizational Affiliation
    • Department of Chemistry, Durham University, Science Laboratories, South Road, Durham, DH1 3LE, U.K.

Macromolecule Content 

  • Total Structure Weight: 16.5 kDa 
  • Atom Count: 1,281 
  • Modeled Residue Count: 138 
  • Deposited Residue Count: 138 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2138Homo sapiensMutation(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
GTEx:  ENSG00000143320 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G9Q
(Subject of Investigation/LOI)

Query on G9Q



Download:Ideal Coordinates CCD File
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

Query on PG4



Download:Ideal Coordinates CCD File
F [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
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 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.689α = 90
b = 47.479β = 90
c = 77.733γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description