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orthosteric ligands

" in MedChemExpress (MCE) Product Catalog:

By Targets:	Adrenergic Receptor (1) ATF6 (1) Cannabinoid Receptor (3) Casein Kinase (1) GABA Receptor (1) Histamine Receptor (1) IKZF Family (1) mAChR (1) Synaptic Vesicle Proteins (1) Wee1 (1)
By Research Areas:	Cancer (1) Neurological Disease (3)

Inhibitors & Agonists

Bibliotecas de Screening

Peptides

Targets Recommended: Ligands for Target Protein for PROTAC Ligands for E3 Ligase

Cat. No.	Nombre del producto	Target	Áreas de investigación	Chemical Structure

HY-158104

LPPM-8	ATF6	Others
LPPM-8 is a ligand of Med25 and an inhibitor of Med25 protein-protein interactions (PPIs). LPPM-8 engages Med25 through interaction with the H2 face of its Activator Interaction Domain and stabilizes full-length protein in the cellular proteome. LPPM-8 is an orthosteric inhibitor of H2-binding transcriptional activators (such as ATF6a). LPPM-8 can be used for studying Med25 and Mediator complex biology .

HY-147559

CB1R Allosteric modulator 2	Cannabinoid Receptor	Others
CB1R Allosteric modulator 2 (compound 18) is a potent CB1R allosteric modulator. CB1R Allosteric modulator 2 shows negatively affects the functional activity of orthosteric ligands (NAM) at CB1Rs .

HY-147558

CB1R Allosteric modulator 1	Cannabinoid Receptor	Others
CB1R Allosteric modulator 1 (compound 11) is a potent CB1R allosteric modulator. CB1R Allosteric modulator 1 shows negatively affects the functional activity of orthosteric ligands (NAM) at CB1Rs .

HY-103513

GABAA receptor agent 2	GABA Receptor	Others
GABAA receptor agent 2 (compound 13) is a compound used to study the structure and orthosteric ligand binding of GABA(A) receptors. The relevant model of GABAA receptor agent 2 can be used to understand the details of orthosteric ligand binding, and a detailed binding mode hypothesis was created through structure-activity relationships with two homologous series of orthosteric GABA(A)R antagonists.

HY-162659

β2AR ligand 1	Adrenergic Receptor	Others
β2AR ligand 1 (Compound 4) is a homobivalent bitopic ligand for β2 adrenergic receptor (β2AR) on the orthosteric binding site (OBS) and the metastable binding sites (MBS) .

HY-122491

Dimethyl-W84 dibromide	mAChR	Neurological Disease
Dimethyl-W84 (dibromide) modulates M2 muscarinic acetylcholine receptors. Dimethyl-W84 (dibromide) can be used in nervous system related research .

HY-144705

GAT564	Cannabinoid Receptor	Neurological Disease
GAT564 (Compound 15d) is a potent allosteric modulator of cannabinoid 1 receptor (CB1R) with EC₅₀s of 87 and 320 nM respectively for cAMP and β-arrestin2. GAT564 markedly promotes orthosteric ligand binding to hCB1R. GAT564 is efficacious as a topical agent that significantly reduces intraocular pressure (IOP) in the ocular normotensive murine model of glaucoma .

HY-124912

VUF-6884	Histamine Receptor	Others
VUF-6884 (Compound 7j) is a histamine receptor (Histamine Receptor) ligand with activity toward human H4R and H1R. Its pEC₅₀ and pK_i values against human H4R are 7.70 and 7.55, respectively, while those against human H1R are 8.17 and 8.11, respectively. VUF-6884 competitively binds to the orthosteric binding site of human H4R to displace histamine, and exhibits inverse agonist activity at human H1R .

HY-180554

UCB1244283	Synaptic Vesicle Proteins	Neurological Disease
UCB1244283 is a synaptic vesicle glycoprotein 2A (SV2A) allosteric modulator. UCB1244283 binds to a secondary ligand-binding site in SV2A and enhances orthosteric ligand engagement when the orthosteric site is occupied, by stabilizing the occluded state and slowing ligand dissociation. UCB1244283 shows a clear protective effect against both tonic and clonic convulsions in sound-sensitive mice. UCB1244283 can be used for epilepsy research .

HY-W1135319

SB-405483	Casein Kinase Wee1 IKZF Family	Cancer
SB-405483 is a CRBN orthosteric ligand bindign enhancer. SB-405483 potentiates degradation of CRBN substrates including CK1α, Wee1, IKZF1/3. SB-405483 stabilizes CRBN and reduces CRBN autoubiquitination. SB-405483 can be used for the research of cancer, such as multiple myeloma and acute myeloid leukemia .

Cat. No.	Nombre del producto

HY-L170

Allosteric Modulators (AMs) Compound Library	250 compounds
An emerging drug design method is based on the secondary binding site effect, where small molecule drugs are designed to bind to secondary binding sites on target biomolecules rather than primary orthomorphic sites. Successful potential drugs (known as allosteric modulators) will be able to bind to allosteric sites and remotely alter (or modify) the conformation of the main orthosteric binding sites of biological targets. Allosteric modulators (AMs) are ligands of proteins that act through binding sites different from natural (orthosteric) ligand sites. AMs are relatively small, more lipophilic, and more rigid compounds. The binding efficacy of AMs with their targets is often slightly lower. AMs are divided into positive AMs (PAMs) and negative AMs (NAMs). AMs are ideal drug targets because they can fine-tune receptor activity while preserving the spatial and temporal signal transduction characteristics of endogenous ligands, resulting in fewer targeted side effects, improved subtype selectivity, and better promotion of biased signal transduction than normal ligands. MCE designs a unique collection of 250 small allosteric modulators. It is a good tool to be used for research on metabolize, cancer and other diseases.

Allosteric Modulators (AMs) Compound Library

250 compounds

An emerging drug design method is based on the secondary binding site effect, where small molecule drugs are designed to bind to secondary binding sites on target biomolecules rather than primary orthomorphic sites. Successful potential drugs (known as allosteric modulators) will be able to bind to allosteric sites and remotely alter (or modify) the conformation of the main orthosteric binding sites of biological targets. Allosteric modulators (AMs) are ligands of proteins that act through binding sites different from natural (orthosteric) ligand sites. AMs are relatively small, more lipophilic, and more rigid compounds. The binding efficacy of AMs with their targets is often slightly lower. AMs are divided into positive AMs (PAMs) and negative AMs (NAMs). AMs are ideal drug targets because they can fine-tune receptor activity while preserving the spatial and temporal signal transduction characteristics of endogenous ligands, resulting in fewer targeted side effects, improved subtype selectivity, and better promotion of biased signal transduction than normal ligands.

MCE designs a unique collection of 250 small allosteric modulators. It is a good tool to be used for research on metabolize, cancer and other diseases.

HY-L928

GPCR Targeted Diversity Library	7,113 compounds
G protein-coupled receptors (GPCRs) are membrane proteins in humans and one of the most important targets in drug discovery. Approximately 35% of launched drugs are targeted GPCRs, making them a crucial class of targets in drug discovery. The orthosteric site of a GPCR is its endogenous ligand’s (such as neurotransmitters or hormones) binding site. This site plays a central role in signal transduction. Small molecules binding to this site typically contain a protonatable amino group, enabling the formation of salt bridges or hydrogen bonds with acidic residues in the binding pocket. In contrast, the allosteric site does not directly initiate signaling but modulates the signal intensity of the GPCR by altering or stabilizing the conformation of the orthosteric site. Small molecules binding to the allosteric site often contain multiple aromatic rings to occupy hydrophobic pockets and achieve their functional effects. MCE has collected over 7,113 reported bioactive molecules targeting GPCRs, covering Class A, B, and C GPCRs. These small molecules were subjected to AI representation to extract 2D and 3D features. Subsequently, we do screening by AI score based on similarity to identify molecules in diversity library highly similar to the reported bioactive molecules in both 2D and 3D, with a threshold greater than 0.7. Further screening based on cLogP was applied to select molecules with good lipophilicity, which facilitates the binding of small molecules to GPCRs. This diversity library can be widely applied to the discovery of compounds targeting GPCR proteins.

GPCR Targeted Diversity Library

7,113 compounds

G protein-coupled receptors (GPCRs) are membrane proteins in humans and one of the most important targets in drug discovery. Approximately 35% of launched drugs are targeted GPCRs, making them a crucial class of targets in drug discovery.

The orthosteric site of a GPCR is its endogenous ligand’s (such as neurotransmitters or hormones) binding site. This site plays a central role in signal transduction. Small molecules binding to this site typically contain a protonatable amino group, enabling the formation of salt bridges or hydrogen bonds with acidic residues in the binding pocket. In contrast, the allosteric site does not directly initiate signaling but modulates the signal intensity of the GPCR by altering or stabilizing the conformation of the orthosteric site. Small molecules binding to the allosteric site often contain multiple aromatic rings to occupy hydrophobic pockets and achieve their functional effects.

MCE has collected over 7,113 reported bioactive molecules targeting GPCRs, covering Class A, B, and C GPCRs. These small molecules were subjected to AI representation to extract 2D and 3D features. Subsequently, we do screening by AI score based on similarity to identify molecules in diversity library highly similar to the reported bioactive molecules in both 2D and 3D, with a threshold greater than 0.7. Further screening based on cLogP was applied to select molecules with good lipophilicity, which facilitates the binding of small molecules to GPCRs. This diversity library can be widely applied to the discovery of compounds targeting GPCR proteins.

HY-L941

Allosteric Modulator Lead‑like Compound Library	4315 compounds
Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery. MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Å², rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets. This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Allosteric Modulator Lead‑like Compound Library

4315 compounds

Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery.

MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Å², rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets.

This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Cat. No.	Nombre del producto	Target	Research Area

HY-158104

LPPM-8	ATF6	Others
LPPM-8 is a ligand of Med25 and an inhibitor of Med25 protein-protein interactions (PPIs). LPPM-8 engages Med25 through interaction with the H2 face of its Activator Interaction Domain and stabilizes full-length protein in the cellular proteome. LPPM-8 is an orthosteric inhibitor of H2-binding transcriptional activators (such as ATF6a). LPPM-8 can be used for studying Med25 and Mediator complex biology .

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BODIPY 493/503 purchased from MedChemExpress. Usage Cited in: Nat Commun. 2025 Feb 1;16(1):1241. [Abstract]

MedchemExpress Validation 01

Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature. Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature. Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature.

BODIPY 493/503 purchased from MedChemExpress. Usage Cited in: Nat Commun. 2025 Feb 1;16(1):1241. [Abstract]

MedchemExpress Validation 01

MedchemExpress Validation 03

Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred

MedchemExpress Validation 04

MedchemExpress Validation

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