4O9S | pdb_00004o9s

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4O9S

Ligand Structure Quality Assessment 


This is version 2.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 52.64 kDa 
  • Atom Count: 3,235 
  • Modeled Residue Count: 349 
  • Deposited Residue Count: 430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinol-binding protein 4
A, B
215Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2RY

Query on 2RY



Download:Ideal Coordinates CCD File
C [auth A],
T [auth B]
1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone
C22 H21 F3 N4 O S
XMIMIFRXLOGETC-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
S [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
HA [auth B],
Q [auth A],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
2RY BindingDB:  4O9S IC50: min: 60, max: 280 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.737α = 90
b = 85.737β = 90
c = 118.806γ = 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
  • Version 2.0: 2020-02-19
    Changes: Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary