9h37

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 9, a novel nanomolar A2A receptor antagonist from modern hit-finding with structure-guided de novo design

Method: X-RAY DIFFRACTION Dmax: 106.1 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Adenosine receptor A2a,Soluble cytochrome b562

Homo sapiens

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 23–127 Not recorded NA SODIUM ION × 1 CLR CHOLESTEROL × 3 OLA OLEIC ACID × 21 A1IR0 2-(furan-2-yl)-7-pyridin-4-yl-pyrrolo[2,3-d]pyrimidin-4-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;0.1 M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Resolution 1.72 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 218–322; UniProt 23–127

Adenosine receptor A2a,Soluble cytochrome b562

Homo sapiens

UniProt P29274

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–208 Chain A; UniProt 219–317 Not recorded NA SODIUM ION × 1 CLR CHOLESTEROL × 3 OLA OLEIC ACID × 21 A1IR0 2-(furan-2-yl)-7-pyridin-4-yl-pyrrolo[2,3-d]pyrimidin-4-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;0.1 M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Resolution 1.72 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

185 other PDB entries and 189 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AA2AR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–217; UniProt 2–208 Author chain A; PDBConstruct 324–422; UniProt 219–317

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9h37

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9h37
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9h37
Deposition date deposition_date2024-10-15
Structure title titleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 9, a novel nanomolar A2A receptor antagonist from modern hit-finding with structure-guided de novo design
Keywords keywordsadenosine receptor, GPCR, antagonist, chemical hit, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.87
Radius of gyration Rg (electron density) rg_electron29.45
Forward intensity I(0) i059605500.00
Molecular weight molecular_weight43938.0 kDa
Excluded volume excluded_volume44421 ų
Envelope volume envelope_volume76780 ų
Hydration-shell volume shell_volume24691 ų
Envelope diameter envelope_diameter110.4
Shell Rg shell_rg32.38
Envelope Rg envelope_rg29.79
Shape Rg shape_rg29.34
Total Rg total_rg29.89
Total atoms total_atoms3356
Residues n_residues385
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax106.1
Rg (real space) rg_real30.38
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real5.9610e+07
I(0) uncertainty (real space) i0_real_error1.0150e+06
Rg (reciprocal space) rg_reciprocal30.16
I(0) (reciprocal space) i0_reciprocal59600000.0000
Solution quality estimate total_estimate0.7578
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.0
Skewness Skewness skewness0.677
Kurtosis Kurtosis kurtosis-0.189
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5873000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.534; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.371; Smooth: 0.879

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)