6Z10 | pdb_00006z10

Crystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in complex with a nanobody and antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.223 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery and Optimization of Novel SUCNR1 Inhibitors: Design of Zwitterionic Derivatives with a Salt Bridge for the Improvement of Oral Exposure.

Velcicky, J.Wilcken, R.Cotesta, S.Janser, P.Schlapbach, A.Wagner, T.Piechon, P.Villard, F.Bouhelal, R.Piller, F.Harlfinger, S.Stringer, R.Fehlmann, D.Kaupmann, K.Littlewood-Evans, A.Haffke, M.Gommermann, N.

(2020) J Med Chem 63: 9856-9875

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01020
  • Primary Citation Related Structures: 
    6Z10

  • PubMed Abstract: 

    G-protein-coupled receptor SUCNR1 (succinate receptor 1 or GPR91) senses the citric cycle intermediate succinate and is implicated in various pathological conditions such as rheumatoid arthritis, liver fibrosis, or obesity. Here, we describe a novel SUCNR1 antagonist scaffold discovered by high-throughput screening. The poor permeation and absorption properties of the most potent compounds, which were zwitterionic in nature, could be improved by the formation of an internal salt bridge, which helped in shielding the two opposite charges and thus also the high polarity of zwitterions with separated charges. The designed compounds containing such a salt bridge reached high oral bioavailability and oral exposure. We believe that this principle could find a broad interest in the medicinal chemistry field as it can be useful not only for the modulation of properties in zwitterionic compounds but also in acidic or basic compounds with poor permeation.


  • Organizational Affiliation
    • Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 60.28 kDa 
  • Atom Count: 3,677 
  • Modeled Residue Count: 412 
  • Deposited Residue Count: 484 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate receptor 1342Rattus norvegicusMutation(s): 2 
Gene Names: Sucnr1Gpr91
Membrane Entity: Yes 
UniProt
Find proteins for Q6IYF9 (Rattus norvegicus)
Explore Q6IYF9 
Go to UniProtKB:  Q6IYF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IYF9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody6142Vicugna pacosMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q4T
(Subject of Investigation/LOI)

Query on Q4T



Download:Ideal Coordinates CCD File
C [auth A]2-[2-[[3-[4-chloranyl-2-fluoranyl-5-[(3~{R})-piperidin-3-yl]oxy-phenyl]-2-fluoranyl-phenyl]carbonylamino]-5-fluoranyl-phenyl]ethanoic acid
C26 H22 Cl F3 N2 O4
MOOARNYDOKGVQG-MRXNPFEDSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
P [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
Q [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.223 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.839α = 90
b = 151.003β = 112.29
c = 68.211γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary