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Conformational analysis

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By Targets:	Bacterial (1) Endogenous Metabolite (1) Phosphodiesterase (PDE) (1) RAR/RXR (1)
By Research Areas:	Cancer (2) Infection (1) Inflammation/Immunology (1)

Inhibitors & Agonists

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Products

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-121125

Aucubigenin	Others	Others
Aucubigenin, the aglycone of the iridoid glycoside aucubin, has been characterized through X-ray diffraction analysis. Its crystal structure reveals monoclinic symmetry with specific conformations adopted by its cyclopentane and pyran rings. The study also determined the absolute configurations of both aucubin and aucubigenin. Significant O-H O hydrogen bonding interactions were observed in the crystal lattices of both compounds, highlighting their structural stability and potential for intermolecular interactions .

HY-119574

GW0791	RAR/RXR	Cancer
GW0791 (Compound 3) is an RXRα agonist with an EC₅₀ of 5 nM. GW0791 can be used for cancer research .

HY-180427

Viscosin	Bacterial Endogenous Metabolite	Infection
Viscosin is a cyclic lipopeptide compound produced by the Pseudomonas genus. Viscosin exerts its antibacterial effect through two mechanisms: membrane permeabilization and interference with cell wall synthesis. Viscosin shows significant antibacterial activity against various Gram-positive bacteria, but has no inhibitory effect on fungi. Viscosin can be used for the study of bacterial infections .

HY-124388

PDE4-IN-20	Phosphodiesterase (PDE)	Inflammation/Immunology
PDE4-IN-20 is a selective submicromolar phosphodiesterase-4 (PDE4) inhibitor with anti-TNF-α properties. PDE4-IN-20 exhibits significant biological activity in vitro and in vivo. The mechanism of action of PDE4-IN-20 is supported by molecular modeling studies, which reveal its binding mode with PDE4. PDE4-IN-20 was optimized in further conformational analysis and showed pharmacological characteristics similar to those of known PDE4 inhibitors .

Cat. No.	Product Name

HY-L942

Allosteric Modulator Fragment Library	1802 compounds
In contrast to the high conservation of conventional orthosteric sites, allosteric sites possess structural characteristics of low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. There is a significant difference between their core structures and orthosteric pockets — allosteric pockets are mostly dynamic grooves formed by protein conformational changes, subunit interface clefts, or shallow depressions, rather than the rigid "keyhole" structure of orthosteric sites. With looser spatial constraints, allosteric sites have the advantages of high selectivity and low off-target risk, and have become an important direction in new drug discovery. Based on the dynamic, hydrophobic, and narrow-long spatial characteristics of allosteric pockets, MCE has performed targeted modification and screening of fragments. The screening criteria strictly conform to the requirements of allosteric binding: molecular weight is controlled at 120–280 Da (to meet the core needs of small molecules in fragment libraries and high derivatization), hydrogen bond donors (HBD ≤ 2), hydrogen bond acceptors (HBA ≤ 3), polar surface area (PSA = 30–80 Å²), rotatable bonds (≤ 2), moderate hydrophobicity (cLogP = 1–3.5), no strongly ionizable groups, and both appropriate rigidity and conformational flexibility to adapt to the dynamic changes of the pocket. Meanwhile, combined with the results of principal moment of inertia (PMI) analysis, fragments with high 3D diversity were obtained. Such fragments have good shape complementarity with allosteric pockets, ensuring that the fragments can smoothly enter the allosteric pockets and form stable binding, while providing room for subsequent optimization and derivation. This library contains 1,800 structurally diverse fragment molecules with excellent drug-like properties, suitable for allosteric drug development and the design and optimization of allosteric sites. It combines the

Allosteric Modulator Fragment Library

1802 compounds

In contrast to the high conservation of conventional orthosteric sites, allosteric sites possess structural characteristics of low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. There is a significant difference between their core structures and orthosteric pockets — allosteric pockets are mostly dynamic grooves formed by protein conformational changes, subunit interface clefts, or shallow depressions, rather than the rigid "keyhole" structure of orthosteric sites. With looser spatial constraints, allosteric sites have the advantages of high selectivity and low off-target risk, and have become an important direction in new drug discovery.

Based on the dynamic, hydrophobic, and narrow-long spatial characteristics of allosteric pockets, MCE has performed targeted modification and screening of fragments. The screening criteria strictly conform to the requirements of allosteric binding: molecular weight is controlled at 120–280 Da (to meet the core needs of small molecules in fragment libraries and high derivatization), hydrogen bond donors (HBD ≤ 2), hydrogen bond acceptors (HBA ≤ 3), polar surface area (PSA = 30–80 Å²), rotatable bonds (≤ 2), moderate hydrophobicity (cLogP = 1–3.5), no strongly ionizable groups, and both appropriate rigidity and conformational flexibility to adapt to the dynamic changes of the pocket. Meanwhile, combined with the results of principal moment of inertia (PMI) analysis, fragments with high 3D diversity were obtained. Such fragments have good shape complementarity with allosteric pockets, ensuring that the fragments can smoothly enter the allosteric pockets and form stable binding, while providing room for subsequent optimization and derivation.

This library contains 1,800 structurally diverse fragment molecules with excellent drug-like properties, suitable for allosteric drug development and the design and optimization of allosteric sites. It combines the

Cat. No.	Product Name	Target	Research Area

HY-P11266

Phakellistatin 13	Peptides	Cancer
Phakellistatin 13 is a natural cycloheptapeptide with anti-tumor activity. Phakellistatin 13 exhibits a potent inhibitory effect on liver cancer cells BEL-7404 (ED₅₀0 < 0.01 μg/mL). Phakellistatin 13 can be used for research on liver cancer .

Cat. No.	Product Name	Category	Target	Chemical Structure

HY-121125

Aucubigenin	Plantaginaceae Iridoids Terpenoids Plants Pseudolysimachion linariifolium subsp. dilatatum (Nakai & Kitag.) D. Y. Hong Source Classification	Others
Aucubigenin, the aglycone of the iridoid glycoside aucubin, has been characterized through X-ray diffraction analysis. Its crystal structure reveals monoclinic symmetry with specific conformations adopted by its cyclopentane and pyran rings. The study also determined the absolute configurations of both aucubin and aucubigenin. Significant O-H O hydrogen bonding interactions were observed in the crystal lattices of both compounds, highlighting their structural stability and potential for intermolecular interactions .

HY-180427

Viscosin	Structural Classification Microorganisms Cyclopeptides Source Classification	Bacterial Endogenous Metabolite
Viscosin is a cyclic lipopeptide compound produced by the Pseudomonas genus. Viscosin exerts its antibacterial effect through two mechanisms: membrane permeabilization and interference with cell wall synthesis. Viscosin shows significant antibacterial activity against various Gram-positive bacteria, but has no inhibitory effect on fungi. Viscosin can be used for the study of bacterial infections .

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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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