This compound belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
External Descriptors
Not available
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.
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Application Protocols
No tested biological assay protocols (e.g., WB, IHC, IF, FC) or recommended dilutions are provided in the Product Data for this small‑molecule reagent.
General laboratory usage suggestions:
Stock solutions: Prepare 10–100 mM in DMSO or MeOH; for aqueous work, prepare 1–10 mg/mL in water or buffer with brief warming and stirring. Filter through 0.2 μm PTFE/nylon prior to analytical injections.
Solid‑phase or immobilization experiments: Convert the serine –OH to an activated carbonate/succinate under mild conditions; couple to amine‑functionalized resins or surfaces. Optimize loading and confirm by elemental analysis or LC‑MS of cleaved test aliquots.
Stress studies: To model DKP formation in peptide formulations, spike known amounts of cyclo(Gly‑Ser) into matrix and analyze by RP‑HPLC‑MS; establish calibration curves and recovery in the specific matrix.
These suggestions are general research practices. For application‑specific parameters (concentrations, incubation times, matrix effects), develop and validate conditions in your laboratory.
Biological Roles
Literature context (general; not item‑specific claims):
Natural occurrence: 2,5‑Diketopiperazines are ubiquitous small cyclic dipeptides found in microorganisms, plants, and processed foods. They can arise from peptide cyclization during biosynthesis or storage/processing.
Structural features: DKPs present a rigid, H‑bond‑rich scaffold that can mimic secondary structural elements of peptides. The serine side chain imparts additional polarity and potential for enzyme recognition compared with fully aliphatic DKPs.
Interactions: DKPs can participate in hydrogen‑bond networks and may bind to proteins or nucleic acids via backbone interactions. Cyclo(Gly‑Ser) lacks bulky hydrophobes; interactions are expected to be dominated by polar contacts.
Metabolic fate (conceptual): Hydrolysis of the diketopiperazine ring under enzymatic or acidic/basic conditions yields the corresponding dipeptide or free amino acids (glycine, serine). Oxidative metabolism can target the primary alcohol of serine.
Analytical relevance: Cyclo(Gly‑Ser) can serve as a reference compound when studying DKP formation from peptides/proteins during storage (e.g., stress testing of peptide formulations) and as a model for transport/uptake studies of small peptidomimetics.
Research use only: Any biological role statements above are mechanistic/biochemical in nature and provided for laboratory research context. No medical or clinical claims are made for this product.
Buffer Applications
Cyclo(-gly-ser) is not a buffering agent and does not define a conventional buffer system.
Practical notes for solution preparation (general):
If aqueous solutions are required, dissolve directly in water or in a minimal volume of DMSO/MeOH, then dilute into neutral buffers (e.g., 10–50 mM phosphate, pH 7.0–7.4). The compound is neutral and will not contribute meaningful buffering capacity.
Avoid strongly acidic or basic buffers at elevated temperature to prevent diketopiperazine ring opening.
If your application requires pH control, select an independent buffer (e.g., phosphate, HEPES, MOPS) appropriate to the target pH and ionic strength, and treat cyclo(Gly‑Ser) as a neutral solute within that system.
Green Alternatives
This product is a solid reagent rather than a process solvent; “green alternatives” predominantly concern solvent choices and reaction conditions during its use.
Preferred solvent choices (general green chemistry guidance):
Water, ethanol, and isopropanol: Favorable EHS profiles and often suitable for dissolution or crystallization of DKPs like cyclo(Gly‑Ser).
2‑MeTHF, CPME: If aprotic media are required, these can substitute for THF/Et2O in some derivatizations but may offer limited solubility for polar DKPs; co‑solvent with alcohol/water may be needed.
Avoid chlorinated solvents (DCM, chloroform) when possible; MeOH/EtOH or ethyl acetate can often replace them for workups and chromatography.
Energy and waste minimization:
Conduct O‑acylations and carbonate formations at ambient temperature in greener solvents (EtOAc/EtOH) using catalytic DMAP and carbonyldiimidazole or organic carbonates, reducing use of acid chlorides.
Use water/EtOH crystallizations instead of normal‑phase silica chromatography to minimize solvent consumption.
Comparison (literature/general):
Water/EtOH vs DMSO/DMF: Greener but sometimes lower solubility; may require mild heating or pH adjustment.
Ethyl acetate vs DCM: Similar polarity for extractions; EtOAc is preferable environmentally but may extract less efficiently—optimize salt content and pH.
Note: Select the green strategy that maintains ring integrity (avoid strong acid/base and high temperatures that induce hydrolysis), balancing EHS benefits against performance.
Pharmaceutical Uses
No pharmacopeial grade or excipient role is specified for this item; it is supplied for research use only.
General formulation/manufacturing context (literature/practice; not item‑specific claims):
DKP occurrence: Diketopiperazines can appear as process‑related impurities or degradation products in peptide drug manufacturing (cyclization of N‑terminal sequences). Cyclo(Gly‑Ser) is a useful reference standard for analytical method development and stability studies aimed at monitoring DKP formation.
Enabling chemistry: The serine –CH2OH permits conjugation (e.g., carbonate, carbamate, succinate) to generate linkers or pro‑moieties in research settings, but any medicinal use requires separate qualification and is outside the scope here.
Analytical control: Methods such as RP‑HPLC with MS detection are commonly validated to track DKPs at low levels in peptide APIs; cyclo(Gly‑Ser) may be used as a system suitability or calibration material in method development.
Regulatory note: No USP/EP/JP monographs or excipient specifications are indicated for this product. For any GMP‑related work, procure appropriate qualified grades and documentation; this Aladdin Scientific product is designated for laboratory research only.
Physical Properties
From Product Data (item-specific):
Appearance: 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.
Literature/General properties for cyclo(Gly‑Ser) and closely related DKPs (reference only, not item specification):
Physical state: Typically a crystalline solid due to strong intermolecular H‑bonding in diketopiperazines; hygroscopicity is generally low to moderate depending on substituents.
Melting point: Often high for DKPs; specific value for cyclo(Gly‑Ser) not compiled across standard handbooks. If critical, confirm experimentally or consult CoA.
Solubility: Moderate in water (improves with slight warming or pH adjustment); readily soluble in polar protic solvents (methanol, ethanol) and DMSO; limited solubility in aprotic, nonpolar solvents (e.g., hexanes, toluene). Hydrogen bonding and the serine –CH2OH enhance aqueous compatibility versus hydrophobic DKPs.
Acid/base behavior: Overall neutral; no strongly ionizable centers under physiological pH. The serine alcohol (pKa ~16–17, literature for primary alcohols) is non-ionizing in water; amide nitrogens are non-basic (conjugated to carbonyls).
Partitioning: Expected low logP (negative to near zero, literature expectation for polar DKPs bearing an alcohol), favoring aqueous/Polar solvent phases.
UV/Vis: Lacks strong chromophores; weak end‑absorption in the far‑UV typical of amides. For quantitative UV work, determine actual ε/λmax experimentally.
Note: When property values are critical (e.g., solubility limits, melting point), verify with a small‑scale test under your laboratory conditions and consult the item’s CoA.
Quality and Grades
From Product Data (item-specific):
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
How to interpret and qualify material (general guidance):
Identity confirmation: For small peptides/DKPs, high‑resolution MS (m/z ~144 [M+H]+, literature), 1H/13C NMR (diagnostic amide carbonyls ~165–175 ppm; α‑CH signals), and IR (amide C=O ~1650–1700 cm⁻¹; O–H stretch ~3300–3500 cm⁻¹) are standard.
Purity assessment: HPLC or UPLC with UV at 210–220 nm (amide absorption) and ELSD/RI as needed. DKPs may have low UV response; adjust detection accordingly.
Residual solvents/metals: Not specified for this item; refer to CoA/Spec Sheet. If application is analytical or sensitive (e.g., catalysis studies), request metal and residual solvent profiles.
Optical purity: Serine is chiral; if stereochemistry matters, verify enantiomeric composition by chiral HPLC or optical rotation. Unless labeled, assume configuration is not specified.
Water content: Not specified for this item; refer to CoA/Spec Sheet. Karl Fischer may be used if hygroscopic uptake is a concern.
Stabilizers/additives: None indicated in Product Data. If formulation components are critical, confirm absence via CoA.
Recommendation: Match assay/purity level and chiral specification to your intended use (e.g., synthesis vs. analytical standard), and archive CoA lot‑specifically for traceability.
Reaction and Applications
As a glycine/serine‑derived 2,5‑diketopiperazine, Cyclo(-gly-ser) is a compact peptidomimetic scaffold with rich hydrogen‑bonding capability and a handle for selective derivatization (serine –CH2OH). Typical laboratory applications include:
Scaffold for peptidomimetics: The DKP ring enforces a β‑turn‑like geometry, useful in designing H‑bonded receptors and foldamers. Substituent effects modulate self‑assembly and crystal engineering.
Organocatalysis/materials: DKPs can act as mild organocatalysts (e.g., H‑bond donors) or as monomers in supramolecular gels; the serine alcohol enables further crosslinking or urethane formation.
Building block for libraries: N‑acylation/alkylation at ring nitrogens and O‑functionalization of the serine side chain enable positional scans. The glycine position allows substitution without introducing additional stereocenters.
Analytical standards: Useful as a model compound for peptide cyclization studies, diketopiperazine formation kinetics, and LC method development for small polar heterocycles.
Probing peptide degradation: DKP formation is a known pathway in peptide/drug degradation; cyclo(Gly‑Ser) serves as a representative DKP artifact for stress studies.
Practical tips:
Protecting group strategies are often unnecessary; however, selective O‑ vs N‑acylation requires choice of base/solvent and acylating reagent (e.g., acyl chlorides/anhydrides).
Maintain neutral to mildly basic conditions to retain ring integrity; strong acids/bases under heat promote ring opening to the dipeptide or amino acids.
For surface attachment, convert the serine alcohol to a reactive carbonate/succinate, or oxidize to the aldehyde/carboxylate, enabling immobilization on resins or surfaces.
Reaction Conditions
Representative literature‑style conditions for common transformations of cyclo(Gly‑Ser) (guidance only; optimize for your system):
N‑Acylation (imide formation):
Reagents: Acyl chloride (1.1–1.5 eq) or anhydride; base (2–3 eq pyridine or DIPEA).
Solvent: DCM, EtOAc, or MeCN; 0–25 °C, 0.5–4 h.
Notes: Minimize moisture; monitor by TLC/HPLC (loss of NH stretch in IR; mass shift +acyl).
N‑Alkylation:
Base: NaH (1.2–2.0 eq) or K2CO3 (2–3 eq) for milder selectivity.
Caution: Competing O‑alkylation on serine –OH; protect as needed.
O‑Acylation (serine alcohol):
Reagents: Acyl anhydrides or chloroformates; base (DMAP catalytic + Et3N).
Solvent: DCM, EtOAc, or MeCN; 0–25 °C.
Selectivity: DMAP promotes O‑acylation; avoid strong base that deprotonates ring nitrogens.
Oxidation of –CH2OH:
DMP (Dess–Martin): CH2Cl2, 0–25 °C, 0.5–2 h → aldehyde.
TEMPO/NaOCl: Biphasic H2O/EtOAc with NaHCO3 buffer, 0–5 °C → aldehyde; NaClO2 can advance to acid.
Hydrolytic ring opening:
Acidic: 1–6 M HCl, 60–100 °C, 1–24 h → dipeptide or amino acids (extended times).
Basic: 1–2 M NaOH, 60–80 °C → analogous outcomes; racemization risk at serine under strong base.
Purification/analysis:
RP‑HPLC (C18) with H2O/MeCN + 0.1% formic acid; detection at 210–220 nm and MS. Avoid high pH eluents for prolonged times to preserve ring.
Yields and kinetics vary with substituents and stereochemistry; run small‑scale screens and confirm structures by NMR/MS.
Safety and Handling
From Product Data (item-specific):
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
Shipping: Normal
General safety guidance (literature/practice; defer to SDS for authoritative information):
Expected hazards: Small neutral cyclic dipeptides typically present low acute toxicity and low volatility; dust may cause mechanical irritation to eyes/respiratory tract.
Personal protective equipment (PPE): Lab coat, safety glasses or goggles, and suitable gloves (e.g., disposable nitrile). Use a dust mask or handle in a fume hood if powder becomes airborne.
Handling: Avoid creating dust. Use clean, dry tools to prevent sample contamination. For weighing, allow solid to equilibrate to room temperature to minimize moisture condensation.
Incompatibilities: Strong oxidizing agents (may oxidize the serine –CH2OH); strong mineral acids or bases under reflux can hydrolyze the diketopiperazine ring (ring opening to dipeptides/constituent amino acids).
First aid (overview):
Inhalation: Move to fresh air; seek medical attention if symptoms persist.
Skin/eye contact: Rinse with water for several minutes; remove contaminated clothing; seek medical advice if irritation continues.
Ingestion: Rinse mouth; do not induce vomiting; obtain medical attention.
Fire safety: Organic solid; use CO2, dry chemical, or water spray. Combustion may produce COx/NOx.
Waste: Dispose according to institutional and local regulations for non‑hazardous organic laboratory chemicals unless SDS indicates otherwise.
Solvent Selection
Cyclo(-gly-ser) is a small, neutral, polar heterocycle (diketopiperazine) with an additional primary alcohol, yielding moderate aqueous affinity and strong H‑bonding.
Polarity/miscibility (literature/general):
Water: Typically moderately soluble; solubility often increases with gentle warming or slight basification (pH 8–9), though the molecule itself remains largely neutral.
Alcohols (MeOH, EtOH, i‑PrOH): Good to excellent solubility; convenient for stock solutions and crystallization trials.
DMSO/DMF: Excellent solvents for concentrated stocks and for reactions (acylation/alkylation). Dilute before bioassays to minimize cosolvent effects.
Acetonitrile/acetone: Moderate solubility; may require small water or alcohol co‑solvent.
Nonpolar solvents (EtOAc, toluene, hexanes): Limited solubility; may be used in biphasic systems or for trituration.
Practical guidance:
Preparing analytical standards: Dissolve in MeOH or H2O:MeOH (1:1) to improve peak shape in reversed‑phase LC; filter (0.2 μm) before injection.
Crystallization: Slow evaporation from aqueous alcohols (EtOH/H2O) often affords well‑formed crystals for X‑ray or purity checks.
Avoid strong acidic/basic solvents if ring integrity must be preserved; prolonged exposure can cause ring opening.
Comparison notes:
Versus more hydrophobic DKPs (e.g., cyclo(Phe‑Phe)), cyclo(Gly‑Ser) is more water compatible and easier to handle in protic media.
Versus linear dipeptides, DKPs are less hygroscopic and often show sharper melting/thermal behavior, aiding sample handling.
Storage and Reconstitution
From Product Data (item-specific):
Storage Conditions: Room temperature
Shipped In: Normal
General guidance (supplemental; not item specification):
Storage: Keep tightly capped in a dry, well‑ventilated place away from heat sources. Protect from strong acids/bases and oxidizers. Store in original container or inert‑lined vial to prevent adsorption.
Stability: DKPs are typically robust at ambient conditions; avoid prolonged exposure to high humidity or elevated temperature if ring integrity is critical.
Reconstitution:
Aqueous: Dissolve in deionized water (1–10 mg/mL) with gentle warming/sonication if needed. If solubility is insufficient, add up to 10–20% MeOH or prepare in buffer (pH 7–8).
Organic: DMSO or MeOH yield concentrated stocks (10–100 mM). Prepare fresh if downstream work is moisture‑sensitive.
Handling after reconstitution: Store solutions at 2–8 °C for short term (hours to days) or aliquot and freeze (−20 °C) for longer term to limit microbial growth and oxidation of the serine alcohol. Minimize freeze–thaw cycles.
Specifications such as water content, peroxide levels, UV cutoff, metal content: Not specified for this item; refer to CoA/Spec Sheet.
Always consult the product’s CoA and SDS for lot‑specific stability, purity, and safety information. Label solutions with preparation date and solvent system for traceability.
Structure and Identity
From Product Data (item-specific):
SKU: C184980
Product Name: Cyclo(-gly-ser)
CAS: 52661-98-0
PubChem CID: 7408485
InChIKey: Not specified for this item; refer to CoA/Spec Sheet. (Provided value appears incomplete in source.)
SMILES: Not specified for this item; refer to CoA/Spec Sheet.
Computed/Literature identity (for reference; not item specification):
Common descriptor: Cyclic dipeptide (2,5-diketopiperazine, DKP) derived from glycine and serine
Molecular formula (literature): C5H8N2O3
Molecular weight (literature): ~144.12 g/mol
Core scaffold: 2,5-diketopiperazine six‑membered ring bearing the serine side chain (–CH2OH) at one α‑carbon; glycine contributes a hydrogen side chain at the other α‑carbon.
Functional groups: Two amide carbonyls (imide-like), two ring nitrogens, one primary alcohol on the serine side chain; multiple H‑bond donors/acceptors.
Stereochemistry: The glycine center is achiral; the serine α‑carbon may be either configuration depending on source (unspecified for this item). The ring itself is typically planar about the amide bonds with limited conformational freedom.
2D structural description (verbal): A six‑membered ring formed by two peptide bonds (–CO–NH–CH(R)–), with carbonyls at positions 2 and 5; one α‑carbon bears –CH2OH (serine), the other bears –H (glycine). This creates a neutral, moderately polar heterocycle capable of intramolecular and intermolecular hydrogen bonding.
Synthetic Utility
Cyclo(-gly-ser) offers multiple, orthogonal handles for derivatization, making it a versatile small‑molecule building block:
Ring nitrogens (N2/N5):
N‑Acylation: Acyl chlorides/anhydrides under mild base (e.g., DIPEA, pyridine) furnish imide‑like N‑acyl DKPs. Reaction rate/selectivity can depend on solvent polarity and temperature.
N‑Alkylation: Via deprotonation (e.g., NaH or K2CO3) in polar aprotic solvents (DMF/DMSO/MeCN) followed by alkyl halides; careful control avoids O‑alkylation of serine.
Serine side chain (–CH2OH):
O‑Acylation/carbamate formation to introduce protecting groups, linkers, or affinity tags.
Oxidation to aldehyde (e.g., Dess–Martin or TEMPO/bleach) or further to acid (e.g., TEMPO/NaClO2), enabling coupling via oxime formation or amide bond formation.
Etherification: Mitsunobu conditions can invert configuration at serine (if stereochemistry is defined), installing various O‑substituents.
Ring transformations:
Hydrolytic ring opening under acidic or basic conditions regenerates the linear dipeptide; useful for controlled release or for late‑stage introduction of terminal functions.
Annulation/cycloaddition: DKP carbonyls can engage in Ugi/Passerini follow‑ups or serve as conformational templates in multicomponent assembly.
Strategic value: The rigid DKP core enforces defined geometry for presenting functional groups in space—useful in receptor mimics, chelating ligands, and surface immobilization. The glycine position avoids added stereochemical complexity, streamlining SAR while the serine alcohol offers tunable polarity.
Target Specificity
Not applicable. This product is a small organic molecule (cyclic dipeptide), not a biological targeting reagent (e.g., antibody, enzyme inhibitor with defined target panel) in this catalog entry. No antigen/epitope, clone, isotype, or species reactivity information is provided in the Product Data.
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