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: 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 ...

    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: zwang@amgen.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinol-binding protein 4B [auth A],
A [auth B]
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02753
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth B],
N [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2WL Binding MOAD:  4PSQ IC50: 440 (nM) from 1 assay(s)
BindingDB:  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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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