3FMZ

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.286 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2T1Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Identification and Characterization of a Non-retinoid Ligand for Retinol-binding Protein 4 Which Lowers Serum Retinol-binding Protein 4 Levels in Vivo.

Motani, A.Wang, Z.Conn, M.Siegler, K.Zhang, Y.Liu, Q.Johnstone, S.Xu, H.Thibault, S.Wang, Y.Fan, P.Connors, R.Le, H.Xu, G.Walker, N.Shan, B.Coward, P.

(2009) J Biol Chem 284: 7673-7680

  • DOI: https://doi.org/10.1074/jbc.M809654200
  • Primary Citation of Related Structures:  
    3FMZ

  • PubMed Abstract: 

    Retinol-binding protein 4 (RBP4) transports retinol from the liver to extrahepatic tissues, and RBP4 lowering is reported to improve insulin sensitivity in mice. We have identified A1120, a high affinity (K(i) = 8.3 nm) non-retinoid ligand for RBP4, which disrupts the interaction between RBP4 and its binding partner transthyretin. Analysis of the RBP4-A1120 co-crystal structure reveals that A1120 induces critical conformational changes at the RBP4-transthyretin interface. Administration of A1120 to mice lowers serum RBP4 and retinol levels but, unexpectedly, does not improve insulin sensitivity. In addition, we show that Rpb4(-/-) mice display normal insulin sensitivity and are not protected from high fat diet-induced insulin resistance. We conclude that lowering RBP4 levels does not improve insulin sensitivity in mice. Therefore, RBP4 lowering may not be an effective strategy for treating diabetes.


  • Organizational Affiliation

    Department of Metabolic Disorders, Amgen, Inc., South San Francisco, California 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinol-binding protein 4
A, B
212Homo sapiensMutation(s): 0 
Gene Names: RBP4PRO2222
UniProt & NIH Common Fund Data Resources
Find proteins for P02753 (Homo sapiens)
Explore P02753 
Go to UniProtKB:  P02753
PHAROS:  P02753
GTEx:  ENSG00000138207 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02753
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2T1
Query on 2T1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid
C20 H19 F3 N2 O3
MEAQCLPMSVEOQF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2T1 BindingDB:  3FMZ IC50: min: 0.16, max: 122 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.286 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.802α = 90
b = 84.802β = 90
c = 119.557γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2T1Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary