DM3 - ≥95% , CAS No.796073-54-6

CAS: 796073-54-6 Cat. No.: D647541 Formula: C₃₇H₅₂ClN₃O₁₀S Molecular Weight: 766.34

GRADE & PURITY ≥95%

Synonyms

HY-130080 | XNG6QZ89ZB | N(2')-Deacetyl-N2-(4-mercapto-4-methyl-1-oxopentyl)-maytansine | SCHEMBL18757725 | Maytansinoid DM3 | DM3 | Maytansine, N2'-deacetyl-N2'-(4-mercapto-1-oxopentyl)- | Maytansinoid DM 3 | UNII-XNG6QZ89ZB

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

DM3 (Maytansinoid DM3) is a maytansine analog bearing disulfide or thiol groups and a tubulin inhibitor, and is a cytotoxic moiety of antibody-drug conjugates (ADCs)

Form:Solid

IC50& Target:Maytansinoids

Specifications

Synonyms

HY-130080 | XNG6QZ89ZB | N(2')-Deacetyl-N2-(4-mercapto-4-methyl-1-oxopentyl)-maytansine | SCHEMBL18757725 | Maytansinoid DM3 | DM3 | Maytansine, N2'-deacetyl-N2'-(4-mercapto-1-oxopentyl)- | Maytansinoid DM 3 | UNII-XNG6QZ89ZB

Specifications & Purity

≥95%

Biochemical and Physiological Mechanisms

DM3 (Maytansinoid DM3) is a maytansine analog bearing disulfide or thiol groups and a tubulin inhibitor, and is a cytotoxic moiety of antibody-drug conjugates (ADCs).

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

This product requires cold chain shipping. Ground and other economy services are not available.

Action Type

INHIBITOR

Purity

≥95%

Names and Identifiers

Canonical Smiles

CC1C2CC(C(C=CC=C(CC3=CC(=C(C(=C3)OC)Cl)N(C(=O)CC(C4(C1O4)C)OC(=O)C(C)N(C)C(=O)CCC(C)S)C)C)OC)(NC(=O)O2)O

IUPAC Name

[(1S,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.110,14.03,5]hexacosa-10,12,14(26),16,18-pentaen-6-yl] (2S)-2-[methyl(4-sulfanylpentanoyl)amino]propanoate

InChIKey

LJFFDOBFKICLHN-IXWHRVGISA-N

INCHI

1S/C37H52ClN3O10S/c1-20-11-10-12-28(48-9)37(46)19-27(49-35(45)39-37)22(3)33-36(5,51-33)29(50-34(44)23(4)40(6)30(42)14-13-21(2)52)18-31(43)41(7)25-16-24(15-20)17-26(47-8)32(25)38/h10-12,16-17,21-23,27-29,33,46,52H,13-15,18-19H2,1-9H3,(H,39,45)/b12-10+,20-11+/t21?,22-,23+,27+,28-,29+,33+,36+,37+/m1/s1

Isomeric SMILES

C[C@@H]1[C@@H]2C[C@]([C@@H](/C=C/C=C(/CC3=CC(=C(C(=C3)OC)Cl)N(C(=O)C[C@@H]([C@]4([C@H]1O4)C)OC(=O)[C@H](C)N(C)C(=O)CCC(C)S)C)\C)OC)(NC(=O)O2)O

Alternate CAS

796073-54-6

Molecular Weight

766.34

Reaxy-Rn

31164895

Reaxys-RN_link_address

https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=31164895&ln=

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Phenylpropanoids and polyketides
    • Class Macrolactams

• Kingdom: Organic compounds
• Superclass: Phenylpropanoids and polyketides
• Class: Macrolactams
• Subclass: Not available
• Intermediate Tree Nodes: Not available
• Direct Parent: Macrolactams
• Alternative Parents: Alpha amino acid esters Alanine and derivatives Anisoles Alkyl aryl ethers 1,3-oxazinanes N-acyl amines Aryl chlorides Tertiary carboxylic acid amides Carbamate esters Lactams Carboxylic acid esters Epoxides Azacyclic compounds Oxacyclic compounds Monocarboxylic acids and derivatives Alkylthiols Alkanolamines Dialkyl ethers Carbonyl compounds Hydrocarbon derivatives Organic oxides Organochlorides
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Alpha-amino acid ester - Macrolactam - Alanine or derivatives - Alpha-amino acid or derivatives - Anisole - Phenol ether - Alkyl aryl ether - 1,3-oxazinane - Aryl chloride - Aryl halide - Benzenoid - N-acyl-amine - Oxazinane - Carbamic acid ester - Tertiary carboxylic acid amide - Carboxamide group - Carboxylic acid ester - Lactam - Alkylthiol - Oxacycle - Azacycle - Organoheterocyclic compound - Carboxylic acid derivative - Dialkyl ether - Oxirane - Ether - Monocarboxylic acid or derivatives - Alkanolamine - Carbonyl group - Organonitrogen compound - Organic oxide - Organochloride - Hydrocarbon derivative - Organooxygen compound - Organohalogen compound - Organic nitrogen compound - Organic oxygen compound - Organosulfur compound - Aromatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.
• 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

Chemical and Physical Properties

• Solubility: DMSO : 100 mg/mL (130.49 mM; ultrasonic and warming and heat to 60°C)

Application Protocols

Only include item-specific validated applications. For DM3 (CAS 796073-54-6):

• Tested applications, recommended use concentrations, and positive controls: Not specified for this item; refer to CoA/Spec Sheet.

General guidance for small-molecule screening (not item-specific):

• Prepare 10–50 mM DMSO stocks; store aliquots at −20°C protected from light. Avoid repeated freeze–thaw cycles.
• Typical assay working concentrations: 0.1–30 µM in final media, ensuring final DMSO ≤0.5–1% v/v (verify assay tolerance).
• Include vehicle controls (matching DMSO), and where possible, use known positive/negative controls to benchmark activity.
• Confirm activity via orthogonal assay formats to rule out detection interference (e.g., redox cycling, fluorescence quenching).

Biological Roles

Item-specific biological role/target information: Not specified for this item; refer to CoA/Spec Sheet.

General considerations (not item-specific; no medical claims):

• As a small molecule within a compound library, DM3 may be used for exploratory biology, including phenotypic screening, target deconvolution, and chemical genetics studies. Without a disclosed structure or annotation, intrinsic biological roles cannot be assigned.
• If/when a target is identified, characterize mechanism through orthogonal assays: binding (SPR/ITC/DSF), functional readouts (enzyme kinetics, reporter assays), and selectivity counterscreens.
• ADME/physicochemical profiling recommended for tool qualification:
  • Solubility (kinetic/thermodynamic), permeability (PAMPA/MDCK), microsomal stability, and protein binding.
  • Redox activity and aggregation checks (e.g., detergent-sensitivity, dynamic light scattering) to rule out artifacts.
• Data provenance: Curate lot-specific characterization and bioactivity metadata in ELNs; ensure reproducibility across passages/cell lines and assay systems.

Research Use Notice (from Product Data): For research use only.

Buffer Applications

Not typically applicable without known ionization properties. No item-specific pKa or buffering capacity is provided for DM3.

General guidance (not item-specific):

• For preparing assay-ready solutions of small molecules:
  • Prepare concentrated stocks in DMSO, then dilute into the assay buffer of choice (e.g., HEPES, Tris, PBS) while maintaining final DMSO below assay tolerance (often ≤0.5–1% v/v).
  • Avoid buffers with reactive nucleophiles or electrophiles if the compound possesses labile functions (unknown here); verify stability by LC–MS over assay time.
• pH considerations:
  • If the compound is acidic or basic (unknown here), solubility and ionization will be pH-dependent. Establish a pH–solubility profile experimentally.
• Filtration (0.2 µm) is recommended to remove particulates prior to biochemical or biophysical measurements.

Green Alternatives

Item-specific solvent and process details are not available for DM3.

General green chemistry considerations for handling small molecules (not item-specific):

• Prefer greener solvents where feasible. Common substitutions (literature):
  • Replace DCM/chloroform with ethyl acetate, 2-MeTHF, cyclopentyl methyl ether (CPME), or dimethyl carbonate (DMC) when polarity and reactivity allow.
  • Replace toluene with anisole or 2-MeTHF in some reactions.
  • Replace DMF/DMAc with propylene carbonate, N-butylpyrrolidone (NBP), or dimethyl isosorbide if compatibility is demonstrated.
• Workup/waste minimization:
  • Use solid-phase extraction (SPE) or minimal-solvent chromatographic methods; explore reverse-phase purification with aqueous-organic systems (MeOH/H2O or MeCN/H2O) to reduce halogenated waste.
  • Implement microscale reactions and DoE to reduce material/solvent consumption during optimization.
• Energy and stability:
  • Store at the recommended −20°C to extend shelf life and minimize repeated synthesis.
  • Use room-temperature catalysis and flow chemistry where possible to reduce energy input.

Tradeoffs:

• Greener solvents may alter selectivity/solubility; validate performance and impurity profiles. Ensure analytical methods are adjusted (e.g., UV cutoff differences, viscosity effects).

Pharmaceutical Uses

Item-specific pharmacopeial status or excipient roles: Not specified for this item; refer to CoA/Spec Sheet.

General, non-clinical context (not item-specific; no therapeutic claims):

• As a research-only small molecule, DM3 is suited for discovery-phase activities, including lead identification and SAR, but is not supplied for human or veterinary use.
• If pursued toward formulation research, typical exploratory approaches include:
  • Solubility enhancement via salts, co-solvents, or amorphous dispersions.
  • Early stability screening (solid-state and in relevant vehicles), pH screening, and photostability.
  • Compatibility testing with common excipients if dosage-form research is contemplated (only in appropriate licensed facilities).
• Regulatory note: Any pharmaceutical development would require comprehensive CMC, tox, and regulatory filings; this product is provided strictly for laboratory research use, as stated in Product Data.

Physical Properties

Item-specific (from 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, pKa, refractive index, UV cutoff: Not specified for this item; refer to CoA/Spec Sheet.

General guidance (literature/practice, not item-specific):

• Small-molecule screening compounds are commonly supplied as solids or concentrated DMSO solutions. If solid, initial dissolution trials typically begin with DMSO (10–50 mM stocks), followed by dilution into aqueous buffers containing 0.1–1% DMSO.
• If the compound has ionizable groups, solubility can often be improved by pH adjustment (acidic solutions for basic amines; basic solutions for phenols/carboxylic acids). Avoid extreme pH if the scaffold is labile (e.g., esters under base; acetals under acid).
• For optical work, determine the UV–Vis profile experimentally to identify absorbance maxima and potential assay interferences (inner-filter effects).
• Hygroscopic or polymorphic behavior, if any, must be confirmed from the CoA or via DSC/TGA and PXRD.

Quality & Grades

Item-specific (from Product Data):

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

General notes on quality (not item-specific):

• For small-molecule library members used in screening, vendors typically provide purity by HPLC/UPLC (area %) with orthogonal identity confirmation (1H NMR, MS/HRMS, sometimes LC–MS retention index). Where available, impurity profiles (residual solvents, isomers) and water content (KF) are listed on the CoA.
• If intended for biochemical screening, a high-purity grade (≥95–98% by HPLC) helps minimize assay artifacts. For analytical method development, ensure UV transparency and low baseline drift (HPLC grade solvents for preparation/analysis).
• Stabilizers/inhibitors: Not specified for this item; if present, they will appear on the CoA and may influence bioassays (e.g., BHT, ascorbate). Remove stabilizers only if compatible with the compound’s stability.
• Batch-to-batch consistency: Verify lot-specific data (purity, form, salt state, residual solvents). For salts vs free base/acid forms, account for counterion content when preparing stock solutions.
• Documentation: Always request and archive the CoA and SDS per lot for regulated environments and reproducibility.

Reaction & Applications

Item-specific synthetic/reactivity notes: Not specified for this item; refer to CoA/Spec Sheet.

General context for library compounds (not item-specific):

• DM3 is listed under a small-molecule/compound library category, suggesting use in screening, target identification, SAR exploration, and probe development.
• Applications typically include:
  • Biochemical and cell-based assay screening (hit-finding, MoA hypotheses).
  • Analytical reference for LC–MS method development and retention model training.
  • Control or competitor compound in binding/functional assays (if orthogonal data are available).
• If the structure is disclosed, synthetic exploitation might include derivatization for SAR: amide coupling, Suzuki/Heck/Sonogashira cross-coupling, N-alkylation/acylation, nucleophilic aromatic substitution, or heteroatom functionalization depending on handles present.
• Practical guidance:
  • Establish stability in DMSO and at assay pH; some scaffolds undergo hydrolysis or oxidation on storage.
  • Perform counter-screens for PAINS features if structure becomes known; verify activity with orthogonal readouts to avoid false positives.
  • Use LC–MS to monitor integrity in assay media over time (t0 vs t_end samples).

Reaction Conditions

Item-specific reaction conditions for DM3 are not provided.

General guidance for small-molecule manipulation (literature-informed, not item-specific):

• Stock preparation: 10–50 mM in dry DMSO; vortex and sonicate as needed. Filter through 0.2 µm PTFE/NY for assay use.
• Stability checks: Incubate at target assay temperature (e.g., 25–37°C) for the assay duration; analyze by LC–MS to confirm <5% degradation.
• If derivatization is planned (structure-dependent):
  • Couplings (amide, Suzuki): 0.1–0.5 M substrate, 0.5–5 mol% Pd catalyst, bases like K2CO3/Cs2CO3, solvents such as MeCN, 2-MeTHF, dioxane/water, 25–100°C, 1–16 h.
  • Reductions/oxidations: Use chemoselective reagents (NaBH4, DIBAL-H, mCPBA) as compatible with functional groups; strictly confirm compatibility first.
• Workup: Quench under cooled, controlled conditions; extract with greener solvents when possible (EtOAc/MTBE) and dry over Na2SO4/MgSO4.
• Expected yields are entirely scaffold- and transformation-dependent; consult primary literature once DM3’s structure is confirmed.

Safety & Handling

Item-specific (from Product Data):

• GHS classification, pictograms, signal word, and H-statements: Not specified for this item; refer to SDS.
• Storage conditions: Store at −20°C.
• Shipping: Ice chest + ice pads.

General laboratory safety (not item-specific; defer to SDS):

• Handle in a chemical fume hood with appropriate PPE: lab coat, safety glasses, and suitable chemical-resistant gloves (e.g., nitrile). Avoid inhalation of dusts/aerosols and contact with skin/eyes.
• Unknown small molecules may present hazards including acute toxicity, skin/eye irritation, or organ toxicity. Until specific hazards are known, treat as harmful.
• Incompatibilities: Avoid strong oxidizers and strong acids/bases until compatibility is confirmed. If the compound is moisture- or air-sensitive, work under dry inert gas and use anhydrous solvents.
• First aid (overview; consult SDS for details):
  • Skin/eye contact: Rinse with water for at least 15 minutes; remove contaminated clothing; seek medical attention.
  • Inhalation: Move to fresh air; monitor breathing; seek medical advice.
  • Ingestion: Rinse mouth; do not induce vomiting unless directed by medical personnel; seek immediate medical attention.
• Spill/accident: Contain with inert absorbent, collect for disposal as hazardous chemical waste according to institutional and local regulations.
• Waste: Dispose through approved hazardous waste streams; do not release to drains.

Solvent Selection

Item-specific solubility: Not specified for this item; refer to CoA/Spec Sheet.

General guidance for small-molecule library compounds (not item-specific):

• Primary stock solvent: DMSO is the default choice for discovery screening due to high solvating power and aqueous compatibility up to ~1–2% v/v in many assays.
• Secondary solvents for preparative work: DMF, DMAc, acetonitrile, methanol/ethanol, THF, or ethyl acetate depending on functional groups. For very nonpolar scaffolds, consider toluene, DCM, or MTBE.
• Aqueous work: Improve apparent solubility via co-solvents (0.1–1% DMSO or ethanol), cyclodextrins, or pH adjustment when ionizable groups exist. Use buffer systems that do not react with the compound (avoid primary amines if acylation-sensitive; avoid nucleophilic buffers for activated esters).
• Dielectric/polarity context (literature values for common solvents):
  • DMSO (ε ~47), DMF (ε ~37), MeCN (ε ~36), MeOH (ε ~33), EtOH (ε ~25), THF (ε ~7.6), toluene (ε ~2.4).
• Practical tips:
  • Assess solubility empirically by incremental solvent addition with sonication and gentle heating (<40°C) as needed.
  • Filter 0.2 µm to remove particulates before bioassays to reduce nonspecific effects.
  • Record concentration by weight and verify by UV/LC if extinction coefficients are unknown.

Storage & Reconstitution

Item-specific (from Product Data):

• Storage: Store at −20°C.
• Shipping: Ice chest + ice pads.

Reconstitution and handling (general, not item-specific):

• If supplied as a solid: Allow vial to equilibrate to room temperature in a desiccator before opening to prevent condensation. Dissolve in anhydrous DMSO to prepare a 10–50 mM stock solution. If aqueous compatibility is required, dilute into buffer with gentle mixing while maintaining final DMSO within assay limits.
• If supplied as a solution: Mix gently, briefly centrifuge, and verify concentration by weight or LC–UV/LC–MS if critical.
• Aliquot to single-use portions to avoid multiple freeze–thaw cycles. Store aliquots tightly sealed under inert gas if the compound is air/moisture sensitive (unknown; verify on CoA/SDS).
• Light and moisture protection: Use amber vials and desiccants when stability is uncertain. Record preparation date and lot.
• Stability: Not specified for this item; confirm by periodic QC (HPLC purity/LC–MS) after storage.

Research Use Notice: For research use only.

Structure & Identity

Item-specific (from Product Data):

• Product name: DM3 (SKU: D647541)
• CAS: 796073-54-6
• PubChem CID: 11578612
• InChIKey: 200897 (as provided; note this is non-standard length — verify on CoA/SDS)
• 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.

General/literature guidance:

• Without a provided structure, functional groups, ring systems, and stereochemistry cannot be summarized. For definitive structural metadata (2D/3D, stereochemistry, and identifiers such as InChI and canonical SMILES), consult the product’s CoA or authoritative databases using the CAS or CID listed above.

How to describe (when structure is available):

• Summarize key motifs (e.g., heteroaromatic cores, halogen substitution, H-bond donors/acceptors), protonation sites, and any stereogenic centers.
• Provide a concise 2D description in words (e.g., “para-disubstituted phenyl linked via amide to a pyridyl ring; tertiary amine side chain”).

Synthetic Utility

Item-specific functional groups and reactivity: Not specified for this item; refer to CoA/Spec Sheet.

General considerations (not item-specific):

• Upon structural disclosure, synthetic utility can be assessed by identifying derivatization handles (halides, boronates, amines, carboxylic acids, nitriles, aldehydes, etc.). These enable:
  • Cross-coupling (Suzuki–Miyaura, Buchwald–Hartwig, Sonogashira) to elaborate aryl/heteroaryl frameworks.
  • Amide bond formation (EDC/HATU/T3P) for analog generation.
  • Nucleophilic substitutions/additions on activated electrophiles or heteroaromatic systems.
  • Late-stage functionalization (C–H activation, Minisci) for rapid diversification.
• Purification and analysis:
  • Use orthogonal chromatography (normal-phase, reverse-phase) and characterize by NMR (1H/13C/heteronuclei), HRMS, and HPLC purity.
• Retrosynthetic planning should account for protecting-group strategy and potential atropisomerism or stereocenter control if present.

Target Specificity

Only include item-specific data. For DM3 (CAS 796073-54-6):

• Target(s), pathway(s), species reactivity, isotype/clone (if applicable): Not specified for this item; refer to CoA/Spec Sheet.

Note: As a small molecule, target specificity would typically be described by binding constants (KD, IC50, EC50) and selectivity panels; none are provided in the Product Data.