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- EMDB-71718: Locally-refined structure of alpha2a adrenergic receptor in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-71718
TitleLocally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905)
Map dataLocal refinement sharpened map of Alpha2a adrenergic receptor in complex with compound 4905
Sample
  • Complex: Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound 4905.
    • Protein or peptide: Alpha-2A adrenergic receptor
  • Ligand: N-(5-methylnaphthalen-1-yl)pyridin-4-amine
KeywordsReceptor / Drug / Complex / GPCR / G-protein / scFv16 / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of uterine smooth muscle contraction / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / alpha-2C adrenergic receptor binding / epinephrine binding / phospholipase C-activating adrenergic receptor signaling pathway / alpha-1B adrenergic receptor binding / negative regulation of norepinephrine secretion / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of epinephrine secretion ...negative regulation of uterine smooth muscle contraction / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / alpha-2C adrenergic receptor binding / epinephrine binding / phospholipase C-activating adrenergic receptor signaling pathway / alpha-1B adrenergic receptor binding / negative regulation of norepinephrine secretion / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of epinephrine secretion / negative regulation of calcium ion-dependent exocytosis / heterotrimeric G-protein binding / response to alcohol / intestinal absorption / positive regulation of potassium ion transport / dopaminergic synapse / thioesterase binding / thermoception / Surfactant metabolism / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / norepinephrine binding / positive regulation of membrane protein ectodomain proteolysis / Adrenoceptors / adrenergic receptor signaling pathway / positive regulation of wound healing / response to morphine / negative regulation of calcium ion transport / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of insulin secretion / Rho protein signal transduction / negative regulation of lipid catabolic process / regulation of vasoconstriction / cellular response to hormone stimulus / adenylate cyclase-activating adrenergic receptor signaling pathway / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / axon terminus / positive regulation of cytokine production / female pregnancy / platelet activation / vasodilation / GABA-ergic synapse / postsynaptic density membrane / epidermal growth factor receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / actin cytoskeleton organization / glucose homeostasis / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G alpha (i) signalling events / DNA replication / basolateral plasma membrane / Ras protein signal transduction / positive regulation of MAPK cascade / signaling receptor complex / positive regulation of cell migration / G protein-coupled receptor signaling pathway / neuronal cell body / positive regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Alpha 2A adrenoceptor / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Alpha-2A adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSrinivasan K / Xu X / Mailhot O / Manglik A / Shoichet B
Funding support United States, 1 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
CitationJournal: bioRxiv / Year: 2026
Title: Toward a Random Background for Ligand Optimization.
Abstract: Ligand optimization is central to drug discovery as hundreds of analogs might be designed and synthesized between an initial hit and a therapeutic candidate. The efficiency of this process is ...Ligand optimization is central to drug discovery as hundreds of analogs might be designed and synthesized between an initial hit and a therapeutic candidate. The efficiency of this process is unclear, at least partly because there is no random background for optimization against which to compare. Such a random background might emerge from synthetically accessible but otherwise systematic random small substitutions across starting ligands, measuring likelihood of achieving a substantial improvement in affinity/potency or other property by any single perturbation. Recent literature and ligand-affinity/potency databases suggest that perhaps 10% of analogs with minor modifications improve upon a parent's potency substantially (by ≥10-fold), but this number is clouded by reporting bias, intentional improvement, and inter-group reproducibility. To begin to establish a background expectation for ligand optimization, we comprehensively and systematically modified 18 lead molecules across six targets with single atom changes; 257 compounds were synthesized. Unexpectedly, 11.2% of these random small perturbation analogs improved potency by ≥10-fold over their parents. Conversely, these more potent analogs typically had worse pharmacokinetics (e.g. reduced metabolic stability, lower plasma free fraction). While it was possible to find analogs where the potency increase compensated for inferior exposure and half-life, resulting in more potent compounds in vivo, overall a frustrated landscape for ligand optimization is revealed. This study begins to establish a background expectation for ligand potency optimization and offers a simple strategy to do so. It also begins to quantify the challenges confronting the field in moving beyond in vitro potency.
History
DepositionJul 15, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71718.png

Downloads & links

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Map

FileDownload / File: emd_71718.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement sharpened map of Alpha2a adrenergic receptor in complex with compound 4905
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 294.804 Å		0.82 Å/pix.
x 360 pix.
= 294.804 Å		0.82 Å/pix.
x 360 pix.
= 294.804 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.745
Minimum - Maximum-5.7650247 - 10.263495000000001
Average (Standard dev.)0.00016280572 (±0.07054063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 294.804 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71718_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Local refinement unsharpened map of Alpha2a adrenergic receptor...

Fileemd_71718_additional_1.map
AnnotationLocal refinement unsharpened map of Alpha2a adrenergic receptor in complex with compound 4905
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map A of Alpha2a adrenergic receptor in...

Fileemd_71718_half_map_1.map
AnnotationHalf Map A of Alpha2a adrenergic receptor in complex with compound 4905
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B of Alpha2a adrenergic receptor in...

Fileemd_71718_half_map_2.map
AnnotationHalf Map B of Alpha2a adrenergic receptor in complex with compound 4905
Projections & Slices
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Sample components

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Entire : Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv...

EntireName: Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound 4905.
Components
  • Complex: Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound 4905.
    • Protein or peptide: Alpha-2A adrenergic receptor
  • Ligand: N-(5-methylnaphthalen-1-yl)pyridin-4-amine

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Supramolecule #1: Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv...

SupramoleculeName: Alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound 4905.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alpha-2A adrenergic receptor

MacromoleculeName: Alpha-2A adrenergic receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.643855 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDASIDFRQ EQPLAEGSFA PMGSLQPDAG NASWNGTEAP GGGARATPYS LQVTLTLVCL AGLLMLLTV FGNVLVIIAV FTSRALKAPQ NLFLVSLASA DILVATLVIP FSLANEVMGY WYFGKAWCEI YLALDVLFCT S SIVHLCAI ...String:
MKTIIALSYI FCLVFADYKD DDDASIDFRQ EQPLAEGSFA PMGSLQPDAG NASWNGTEAP GGGARATPYS LQVTLTLVCL AGLLMLLTV FGNVLVIIAV FTSRALKAPQ NLFLVSLASA DILVATLVIP FSLANEVMGY WYFGKAWCEI YLALDVLFCT S SIVHLCAI SLDRYWSITQ AIEYNLKRTP RRIKAIIITV WVISAVISFP PLISIEKKGG GGGPQPAEPR CEINDQKWYV IS SCIGSFF APCLIMILVY VRIYQIAKRR TRVPPSRRGP DAVAAPPGGT ERRPNGLGPE RSAGPGGAEA EPLPTQLNGA PGE PAPAGP RDTDALDLEE SSSSDHAERP PGPRRPERGP RGKGKARASQ VKPGDSLPRR GPGATGIGTP AAGPGEERVG AAKA SRWRG RQNREKRFTF VLAVVIGVFV VCWFPFFFTY TLTAVGCSVP RTLFKFFFWF GYCNSSLNPV IYTIFNHDFR RAFKK ILCR GDRKRIV

UniProtKB: Alpha-2A adrenergic receptor

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Macromolecule #2: N-(5-methylnaphthalen-1-yl)pyridin-4-amine

MacromoleculeName: N-(5-methylnaphthalen-1-yl)pyridin-4-amine / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1CIU
Molecular weightTheoretical: 234.296 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClSodium chloride
0.0075 % w/vC47H88O22Lauryl Maltose Neopentyl Glycol
0.0025 % w/vC56H92O25Glyco-diosgenin
0.001 % w/vC31H50O4Cholesteryl hemisuccinate
0.01 mMC16H14N2N-(5-methylnaphthalen-1-yl)pyridin-4-amine

Details: CHS was solubilized in LMNG and GDN prior to diluting into buffers.
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Details: 15 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10305 / Average exposure time: 2.0 sec. / Average electron dose: 0.596 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6609807
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: De-novo map generation
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 323827
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ej8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 110.6
Output model

PDB-9pln:
Locally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905)

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