7PX4 | pdb_00007px4

Crystal structure of the adenosine A2A receptor (A2A-PSB1-bRIL) in complex with preladenant conjugate PSB-2113


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PX4

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A 2A Receptor with Preladenant Conjugates.

Claff, T.Klapschinski, T.A.Tiruttani Subhramanyam, U.K.Vaassen, V.J.Schlegel, J.G.Vielmuth, C.Voss, J.H.Labahn, J.Muller, C.E.

(2022) Angew Chem Int Ed Engl 61: e202115545-e202115545

  • DOI: https://doi.org/10.1002/anie.202115545
  • Primary Citation Related Structures: 
    7PX4, 7PYR

  • PubMed Abstract: 

    The G protein-coupled adenosine A 2A receptor (A 2A AR) is an important new (potential) drug target in immuno-oncology, and for neurodegenerative diseases. Preladenant and its derivatives belong to the most potent A 2A AR antagonists displaying exceptional selectivity. While crystal structures of the human A 2A AR have been solved, mostly using the A 2A -StaR2 protein that bears 9 point mutations, co-crystallization with Preladenant derivatives has so far been elusive. We developed a new A 2A AR construct harboring a single point mutation (S91 3.39 K) which renders it extremely thermostable. This allowed the co-crystallization of two novel Preladenant derivatives, the polyethylene glycol-conjugated (PEGylated) PSB-2113, and the fluorophore-labeled PSB-2115. The obtained crystal structures (2.25 Å and 2.6 Å resolution) provide explanations for the high potency and selectivity of Preladenant derivatives. They represent the first crystal structures of a GPCR in complex with PEG- and fluorophore-conjugated ligands. The applied strategy is predicted to be applicable to further class A GPCRs.


  • Organizational Affiliation
    • Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.

Macromolecule Content 

  • Total Structure Weight: 60.6 kDa 
  • Atom Count: 3,813 
  • Modeled Residue Count: 390 
  • Deposited Residue Count: 447 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a447Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: ADORA2AADORA2cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29274
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8E2
(Subject of Investigation/LOI)

Query on 8E2



Download:Ideal Coordinates CCD File
E [auth A]Preladenant conjugate PSB-2113
C38 H52 N10 O9
BIWDHFUPTSCUTC-UHFFFAOYSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
FA [auth A],
GA [auth A],
HA [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [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],
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]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG

Query on PEG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.6α = 90
b = 180.262β = 90
c = 139.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1328
German Research Foundation (DFG)GermanyFOR2327
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary