4O9S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4.

Wang, Y.Connors, R.Fan, P.Wang, X.Wang, Z.Liu, J.Kayser, F.Medina, J.C.Johnstone, S.Xu, H.Thibault, S.Walker, N.Conn, M.Zhang, Y.Liu, Q.Grillo, M.P.Motani, A.Coward, P.Wang, Z.

(2014) Bioorg.Med.Chem.Lett. 24: 2885-2891

  • DOI: 10.1016/j.bmcl.2014.04.089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retinol-Binding Protein 4 (RBP4) is a plasma protein that transports retinol (vitamin A) from the liver to peripheral tissues. This Letter highlights our efforts in discovering the first, to our knowledge, non-retinoid small molecules that bind to RB ...

    Retinol-Binding Protein 4 (RBP4) is a plasma protein that transports retinol (vitamin A) from the liver to peripheral tissues. This Letter highlights our efforts in discovering the first, to our knowledge, non-retinoid small molecules that bind to RBP4 at the retinol site and reduce serum RBP4 levels in mice, by disrupting the interaction between RBP4 and transthyretin (TTR), a plasma protein that binds RBP4 and protects it from renal excretion. Potent compounds were discovered and optimized quickly from high-throughput screen (HTS) hits utilizing a structure-based approach. Inhibitor co-crystal X-ray structures revealed unique disruptions of RBP4-TTR interactions by our compounds through induced loop conformational changes instead of steric hindrance exemplified by fenretinide. When administered to mice, A1120, a representative compound in the series, showed concentration-dependent retinol and RBP4 lowering.


    Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA. Electronic address: yingcai02@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinol-binding protein 4
A, B
215Homo sapiensMutation(s): 0 
Gene Names: RBP4
Find proteins for P02753 (Homo sapiens)
Go to Gene View: RBP4
Go to UniProtKB:  P02753
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2RY
Query on 2RY

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A, B
1-[4-(8lambda~4~-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone
C22 H19 F3 N4 O S
CMNSBUJAOPBGKR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2RYIC50: 280 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 85.737α = 90.00
b = 85.737β = 90.00
c = 118.806γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
ADSCdata collection
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release