SQ-609 , CAS No.627052-25-9

CAS: 627052-25-9 Cat. No.: S669789 Formula: C₂₂H₃₈N₂O Molecular Weight: 346.5 PubChem CID: 9841182

Storage

Room temperature

Specifications

Storage

Room temperature

Product Properties

ALogP

3.8

Names and Identifiers

Canonical Smiles

OC1CCN(CC2CCN(CC34CC5CC(CC(C5)C3)C4)CC2)CC1

IUPAC Name

1-[[1-(1-adamantylmethyl)piperidin-4-yl]methyl]piperidin-4-ol

InChIKey

YUBKDPOCUHUSLW-UHFFFAOYSA-N

INCHI

1S/C22H38N2O/c25-21-3-7-23(8-4-21)15-17-1-5-24(6-2-17)16-22-12-18-9-19(13-22)11-20(10-18)14-22/h17-21,25H,1-16H2

Isomeric SMILES

C1CN(CCC1CN2CCC(CC2)O)CC34CC5CC(C3)CC(C5)C4

PubChem CID

9841182

Molecular Weight

346.5

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Class Piperidines

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Class: Piperidines
• Subclass: Not available
• Intermediate Tree Nodes: Not available
• Direct Parent: Piperidines
• Alternative Parents: Trialkylamines Secondary alcohols Azacyclic compounds Hydrocarbon derivatives
• Molecular Framework: Aliphatic heteropolycyclic compounds
• Substituents: Piperidine - Tertiary aliphatic amine - Tertiary amine - Secondary alcohol - Azacycle - Organic nitrogen compound - Organic oxygen compound - Hydrocarbon derivative - Organooxygen compound - Organonitrogen compound - Amine - Alcohol - Aliphatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as piperidines. These are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.
• External Descriptors: Not available

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Associated Targets(non-human)

Mycobacterium tuberculosis (203094 Activities)

Explore this target

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

Mechanisms of Action

Chemical and Physical Properties

• Molecular Weight: 346.500 g/mol
• XLogP3: 3.800
• Hydrogen Bond Donor Count: 1
• Hydrogen Bond Acceptor Count: 3
• Rotatable Bond Count: 4
• Exact Mass: 346.298 Da
• Monoisotopic Mass: 346.298 Da
• Topological Polar Surface Area: 26.700 Ų
• Heavy Atom Count: 25
• Formal Charge: 0
• Complexity: 421.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 0
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

Application Protocols

No item-specific, validated protocols are supplied in the Product Data. The following are general, non-binding guidelines for handling small-molecule library compounds in screening.

• Stock preparation (general)

  • Weigh solid quickly in low humidity. Prepare 10–50 mM stock in anhydrous DMSO; sonicate if needed. Record exact concentration by weight-in or by quantitative NMR if required.
  • Aliquot into low-bind tubes or plates to minimize freeze–thaw cycles; label with SKU S669789, CAS 627052-25-9, lot, and date.

• Assay dilution

  • Prepare serial dilutions in DMSO, then back-dilute into assay buffer to the desired final concentration, keeping final DMSO constant (e.g., 0.1–0.5% v/v).
  • Include vehicle controls, positive/negative controls, and assay interference controls (detergent, redox quenchers) as relevant.

• Analytical verification

  • Confirm identity/purity by LC–MS prior to screening; re-check active wells post-assay to confirm integrity.

• Data capture

  • Store raw and processed data with compound identifiers and plate maps. Use barcodes to ensure traceability.

Refer to the SDS and CoA for any item-specific preparation or handling notes once available.

Biological Roles

No biological target or mechanism is provided for this item. The content below outlines general considerations for small molecules used as research tools.

• Item-specific (Product Data)

  • Target/Pathway: Not specified for this item; refer to CoA/Spec Sheet or primary literature.

• General guidance (not item-specific)

  • Small molecules can serve as chemical probes to modulate enzymatic pathways, receptors, transporters, or protein–protein interactions, enabling functional studies and target validation.
  • For phenotypic screens, deconvolution strategies include chemoproteomics, CRISPR modifier screens, transcriptional profiling, and testing against panels of recombinant targets.
  • Establish selectivity by counterscreening against related isoforms and measuring off-target panels (e.g., kinases, GPCRs) when relevant.
  • Evaluate redox activity, fluorescence, or aggregation tendencies that can confound assays; include appropriate controls (detergent, albumin, redox quenchers).

• Data robustness

  • Use orthogonal assay formats (biochemical vs. cellular vs. biophysical) to corroborate observed effects.
  • Confirm compound integrity by LC–MS before and after assays to rule out degradation-driven artifacts.

Research Use Note: For research use only. Not for human or veterinary use.

Buffer Applications

This item is a small-molecule screening compound rather than a buffering agent. Therefore classical buffer system design (e.g., phosphate, Tris, HEPES) does not apply directly.

• Practical notes for assay solutions (general)

  • Prepare concentrated stocks in DMSO (typically 10–50 mM), then dilute into assay buffer, keeping final DMSO constant across control and treated wells.
  • Common assay buffers: HEPES, PBS, Tris-buffered saline; choose based on biological system and avoid components that chelate metals or react with the compound once structure is known.
  • To mitigate precipitation, pre-warm buffers and add compound last with thorough mixing; consider 0.01–0.05% nonionic surfactant if assay-compatible.
  • For pH-sensitive compounds, use buffers with adequate capacity around the assay pH and avoid strong nucleophiles or oxidants.

• Filtration and sterility

  • If sterility is required, filter final working solutions through 0.2 µm PTFE/nylon filters; confirm no adsorption losses.

Item-specific buffer pKa/pH ranges: Not specified for this item; refer to CoA/Spec Sheet once structural ionization is known.

Green Alternatives

In the absence of item-specific solvent requirements, greener practices can be implemented around solution preparation and workups.

• Greener solvent options (general)

  • For stock solutions: consider Cyrene (dihydrolevoglucosenone) or propylene carbonate as partial substitutes for DMF/NMP when compatible with the compound.
  • For synthetic operations (if applicable): 2-MeTHF or CPME can substitute for THF/Et2O in many transformations; EtOAc can replace DCM for extractions.

• Comparison (general, literature)

  • DMSO vs Cyrene: DMSO is broadly bioassay-compatible; Cyrene offers improved environmental profile but higher viscosity and different polarity—evaluate solubility and assay tolerance.
  • Acetonitrile vs EtOH/IPA: ACN is excellent for LC–MS; ethanol or isopropanol are greener for preparative work if sensitivity allows.

• Practical implementation

  • Start with small-scale solubility checks in greener candidates; confirm no assay interference.
  • Use minimal DMSO percentage in assay wells (e.g., ≤0.1–0.5% v/v where possible) and standardize across controls to reduce variability.
  • Apply microplate sealing to reduce DMSO evaporation and waste.

Note: These recommendations are general; confirm compatibility once the compound’s structure and stability profile are available.

Pharmaceutical Uses

No pharmacopeial or excipient status is provided for this item. The product is intended for research use only.

• Item-specific (Product Data)

  • Regulatory/pharmacopeial status: Not specified for this item; refer to CoA/Spec Sheet.

• General context (not item-specific)

  • In discovery settings, small molecules may be used as reference materials, internal standards, or tool compounds in preclinical research. Any use in GMP manufacturing or clinical development would require appropriate qualification, specifications, and documentation.
  • For preformulation studies, characterize solid form, solubility profile (pH/vehicle), and stability (thermal, oxidative, photolytic) prior to in vivo research.

• Formulation research practices

  • For in vitro dosing, DMSO stocks diluted into aqueous media are common; for in vivo research vehicles (where permitted by institutional review), cosolvent or lipid-based systems may be explored—ensure all uses remain within research-only parameters and institutional approvals.

No therapeutic claims are made. This product is provided strictly for laboratory research use.

Physical Properties

Item-specific values are not provided in the Product Data. Do not assume specifications; confirm via CoA/Spec Sheet or SDS.

• Item-specific (Product Data)

  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
  • Melting point (MP): Not specified for this item; refer to CoA/Spec Sheet.
  • Boiling point (BP): Not specified for this item; refer to CoA/Spec Sheet.
  • Density: Not specified for this item; refer to CoA/Spec Sheet.
  • Solubility: Not specified for this item; refer to CoA/Spec Sheet.
  • LogP/logD: Not specified for this item; refer to CoA/Spec Sheet.
  • Refractive index: Not applicable/unknown for solids; Not specified for this item; refer to CoA/Spec Sheet.

• General guidance (literature/computed, not item-specific)

  • Library screening compounds are commonly supplied as crystalline solids or powders with variable solubility in aqueous media; DMSO is the standard stock solvent when chemistry permits.
  • If the compound contains ionizable groups, solubility can often be improved by salt formation or pH adjustment (for example, acetate or HCl salts for basic amines; Na/TEA salts for acids). Verify compatibility with assays.
  • Establish a solubility limit by small-scale titration in DMSO and common cosolvents (MeOH, EtOH, acetonitrile, 2-MeTHF, propylene carbonate). Filter through 0.2 µm if particulates persist.

Quality & Grades

Quality designations and purity are not provided in the Product Data for this SKU. Do not infer unstated specifications.

• Item-specific (Product Data)

  • Grade/purity: Not specified for this item; refer to CoA/Spec Sheet.
  • Stabilizer/additives: Not specified for this item; refer to CoA/Spec Sheet.

• Guidance on grades (general, not item-specific)

  • Screening/library grade compounds are typically suitable for discovery biology, HTS, and chemistry optimization; they may not meet low-UV or trace-metal limits associated with chromatography- or semiconductor-grade reagents.
  • If the compound will be used as an analytical reference standard, request a CoA including purity by qNMR or HPLC/UPLC with orthogonal detection, water content (Karl Fischer), and residual solvent profile.
  • Stabilizers (if present) can influence bioassays and chromatograms; confirm absence/presence before critical use.

• Practical QA tips

  • Verify identity by LC–MS and, when feasible, by 1H NMR prior to key studies.
  • Record lot number and retain a reserve sample for future cross-checks, especially for SAR or lead-optimization campaigns.

Reaction & Applications

This product is categorized as a small-molecule library member for research screening. Without a disclosed structure, synthetic reactivity cannot be detailed. The following focuses on research applications and handling in discovery workflows.

• Screening applications (general)

  • Suitable for primary HTS, hit confirmation, and early SAR when structure and purity are verified.
  • Use in phenotypic assays or target-based biochemical assays, followed by orthogonal counterscreens (aggregation, redox cycling, luciferase interference) to de-risk artifacts.

• Assay development tips

  • Establish solubility and stability in DMSO and assay buffers; perform time-course LC–MS to assess degradation.
  • Check for pan-assay interference (PAINS) motifs and reactive functionalities once structure is available; apply detergent- and redox-based controls.

• Data integrity

  • Track compound via SKU S669789 and CAS 627052-25-9; capture lot-specific purity and storage history.
  • Employ dose–response curves with at least 10–12 points over 3–4 log units; confirm activity in independent replicates.

• Follow-up chemistry

  • When identity is confirmed, design analogs to probe physicochemical space (lipophilicity, polarity, HBD/HBA) to optimize potency and ADME properties.

Reaction Conditions

Not applicable without a disclosed structure and functional-group profile. No reaction conditions are specified for this item in the Product Data.

• Item-specific (Product Data)

  • Named reactions/catalysts/solvents/temperatures: Not specified for this item; refer to CoA/Spec Sheet.

• General note

  • If the compound is later used as a substrate or intermediate, establish stability windows (temperature, pH, light, oxidants/reductants) by small-scale scouting experiments and analytical monitoring (LC–MS, TLC, NMR).

Safety & Handling

Always defer to the SDS for authoritative safety information. No item-specific hazard classifications are provided in the Product Data.

• Item-specific (Product Data)

  • GHS classification: Not specified for this item; refer to SDS.
  • Signal word / H-statements / Pictograms: Not specified for this item; refer to SDS.
  • Storage conditions: Room temperature.

• General laboratory precautions (not item-specific)

  • Use appropriate PPE: lab coat, safety glasses, and suitable gloves (e.g., nitrile). Handle powders in a fume hood to avoid inhalation.
  • Avoid contact with oxidizers/reducing agents and strong acids/bases until compatibility is known. Keep containers tightly closed and protected from moisture.
  • If preparing DMSO stocks, prevent skin contact; DMSO can facilitate dermal absorption of solutes.

• First aid overview (general)

  • Inhalation: Move to fresh air; seek medical attention if symptoms occur.
  • Skin/eye contact: Rinse with water for at least 15 minutes; remove contaminated clothing; obtain medical advice.
  • Ingestion: Rinse mouth; seek medical attention. Do not induce vomiting unless directed by medical personnel.

• Waste/disposal (general)

  • Collect organic waste following institutional guidelines. Do not dispose to drain. Label waste streams clearly if halogenated solvents are used.

Solvent Selection

Because item-specific solubility data are not provided, initial compatibility screening is recommended. The following is general guidance for small-molecule library compounds.

• Primary stock solvent (general practice)

  • DMSO is the default due to broad solvency and assay compatibility up to 0.1–1% v/v in many biochemical and cell-based assays.

• Cosolvent strategies

  • For hydrophobic compounds: consider NMP, DMF, acetonitrile, 2-MeTHF, or propylene carbonate for concentrated intermediates; dilute into aqueous buffers with surfactants (e.g., 0.01–0.1% Tween 80) if assay-tolerated.
  • For ionizable compounds: adjust pH to improve aqueous solubility (use volatile buffers for MS compatibility).

• Small comparison (general)

  • DMSO: very high polarity/proticity index; miscible with water; excellent solvency; widely assay-compatible.
  • Acetonitrile: polar aprotic; lower viscosity; MS-friendly; limited water tolerance for highly lipophilic analytes.
  • 2-MeTHF/CPME: greener ethers; useful for chemical prep or extraction but less common for bioassay stocks.

• Practical tips

  • Determine a maximum non-precipitating DMSO percentage for your assay matrix by turbidity or DLS checks.
  • Filter sterilize stock solutions if asepsis is required; confirm compound stability against hydrolysis/oxidation under chosen solvent conditions.

Storage & Reconstitution

• Item-specific (Product Data)

  • Storage conditions: Room temperature.
  • Shipped in: Not specified for this item; refer to CoA/Spec Sheet.
  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.

• General storage guidance (not item-specific)

  • Keep container tightly closed in a dry, well-ventilated place away from direct light. Use a desiccator or inert-gas backfill if moisture/oxygen sensitivity is suspected.
  • For solution stocks (e.g., in DMSO), prepare single-use aliquots and store at −20 to −80°C to minimize degradation and freeze–thaw cycles; equilibrate to room temperature before opening to reduce condensation.
  • Periodically assess integrity by LC–MS/UPLC. Discard solutions showing precipitation, color change, or degradation peaks.

• Reconstitution (general)

  • If supplied as a solid, begin with DMSO to a convenient concentration (e.g., 10–50 mM), then dilute with compatible media immediately prior to use.
  • If poor solubility is observed, consider gentle warming (≤40°C) and brief sonication; avoid prolonged heating or basic conditions unless stability is known.

Research Use Note: For research use only. Not for human or veterinary use.

Structure & Identity

Overview: SQ-609 is listed as a small-molecule library member intended for research screening. Item-specific structural identifiers are not provided in the Product Data.

• Item-specific (Product Data)

  • Chemical name: Not specified for this item; refer to CoA/Spec Sheet.
  • CAS: 627052-25-9
  • InChIKey: Not specified for this item; refer to CoA/Spec Sheet. (The short numeric “446960” provided is not a standard InChIKey format.)
  • SMILES: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

• Structural features (general guidance)

  • Without a provided structure, specific functional groups, ring systems, or stereochemistry cannot be described for this item.
  • For experimental planning, consult the CoA/SDS to confirm heteroatoms (N, O, S, halogens), ionizable centers, and any stereogenic elements that may impact solubility and assay behavior.

• Practical notes

  • If structure is later confirmed, derive calculated properties (cLogP, pKa predictions) to guide solvent selection and formulation.
  • Register this compound in ELN/LIMS with CAS and SKU (S669789) and link to assay metadata for traceability.

Synthetic Utility

Specific synthetic applications cannot be described without a known structure. No functional groups or reactivity patterns are available in the Product Data.

• Item-specific (Product Data)

  • Functional groups/reactivity: Not specified for this item; refer to CoA/Spec Sheet.

• General guidance (not item-specific)

  • If the structure becomes available, map reactive handles (e.g., aryl halides for cross-coupling, amines/acids for amide coupling) to plan analog synthesis for SAR.
  • Protecting-group considerations, chemoselectivity, and orthogonal coupling strategies should be tailored to the confirmed scaffold.

• Practical next steps

  • Upon structural confirmation, generate a retrosynthetic plan and identify convergent routes, enabling rapid analog expansion for medicinal chemistry campaigns.

Target Specificity

No biological target, pathway, or selectivity profile is provided for this item.

• Item-specific (Product Data)

  • Target/class: Not specified for this item; refer to CoA/Spec Sheet.
  • Species selectivity: Not specified for this item; refer to CoA/Spec Sheet.
  • Off-targets/panels: Not specified for this item; refer to CoA/Spec Sheet.

• General guidance (not item-specific)

  • Establish target engagement with orthogonal methods (biochemical potency, cellular biomarker modulation, biophysical binding such as SPR/ITC/DSF).
  • Build a selectivity matrix across related family members and relevant safety targets before drawing mechanistic conclusions.

Frequently Asked Questions

How should this product be stored?

Store at room temperature.

What are the CAS number, molecular formula and molecular weight?

The CAS Number is 627052-25-9, the molecular formula is C22H38N2O, and the molecular weight is 346.5 g/mol. InChIKey YUBKDPOCUHUSLW-UHFFFAOYSA-N.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.