4PSQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.bmcl.2014.04.089
  • Primary Citation of Related Structures:  
    4O9S, 4PSQ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinol-binding protein 4A [auth B],
B [auth A]
212Homo sapiensMutation(s): 0 
Gene Names: RBP4PRO2222
Membrane Entity: Yes 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2WL
Query on 2WL

Download Ideal Coordinates CCD File 
C [auth B],
M [auth A]
(1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone
C21 H21 Cl N4 O
ITFKVPSANNTLSY-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth B],
N [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
H [auth B]
I [auth B]
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2WL BindingDB:  4PSQ IC50: 440 (nM) from 1 assay(s)
Binding MOAD:  4PSQ IC50: 440 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.531α = 90
b = 96.531β = 90
c = 118.072γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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