7AA1

Structural comparison of cellular retinoic acid binding proteins I and II in the presence and absence of natural and synthetic ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 ?
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands.

Tomlinson, C.W.E.Cornish, K.A.S.Whiting, A.Pohl, E.

(2021) Acta Crystallogr D Struct Biol 77: 164-175

  • DOI: https://doi.org/10.1107/S2059798320015247
  • Primary Citation of Related Structures:  
    7A9Y, 7A9Z, 7AA0, 7AA1

  • PubMed Abstract: 

    A detailed understanding of the interactions between small-molecule ligands and their proposed binding targets is of the utmost importance for modern drug-development programs. Cellular retinoic acid-binding proteins I and II (CRABPI and CRABPII) facilitate a number of vital retinoid signalling pathways in mammalian cells and offer a gateway to manipulation of signalling that could potentially reduce phenotypes in serious diseases, including cancer and neurodegeneration. Although structurally very similar, the two proteins possess distinctly different biological functions, with their signalling influence being exerted through both genomic and nongenomic pathways. In this article, crystal structures are presented of the L29C mutant of Homo sapiens CRABPI in complex with naturally occurring fatty acids (1.64?? resolution) and with the synthetic retinoid DC645 (2.41?? resolution), and of CRABPII in complex with the ligands DC479 (1.80?? resolution) and DC645 (1.71?? resolution). DC645 and DC479 are two potential drug compounds identified in a recent synthetic retinoid development program. In particular, DC645 has recently been shown to have disease-modifying capabilities in neurodegenerative disease models by activating both genomic and nongenomic signalling pathways. These co-crystal structures demonstrate a canonical binding behaviour akin to that exhibited with all-trans-retinoic acid and help to explain how the compounds are able to exert an influence on part of the retinoid signalling cascade.


  • Organizational Affiliation

    Department of Chemistry, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2A [auth AAA]138Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R62 (Subject of Investigation/LOI)
Query on R62

Download Ideal Coordinates CCD File 
B [auth AAA]4-[2-(5,5,8,8-tetramethyl-6,7-dihydroquinoxalin-2-yl)ethynyl]benzoic acid
C21 H22 N2 O2
BUYUFJZVMVFQLQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 ?
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • Space Group: P 21 3
Unit Cell:
Length ( ? )Angle ( ? )
a = 78.56¦Á = 90
b = 78.56¦Â = 90
c = 78.56¦Ă = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata reduction
XDSdata processing
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-12-01
    Changes: Database references, Structure summary
  • Version 1.3: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
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