Guanosine 5'-diphosphate

 CAS No.: 146-91-8  Cat No.: BP-300091  Purity: ≥95% by HPLC 4.5  

Guanosine 5'-diphosphate is an endogenous nucleotide ligand that binds guanine nucleotide-dependent proteins, including GTPases and nucleotide-processing enzymes. It is not a standard PROTAC warhead for selective degradation of a single protein target, but it can serve as a biochemical recognition motif in studies involving nucleotide-binding pockets. In a targeted degradation concept, a guanosine diphosphate-derived ligand would require careful validation of target selectivity and a linker-tolerant attachment site that preserves nucleotide recognition. Coupling such a motif to an E3 ligase recruiter could, in principle, test whether nucleotide-binding proteins can be brought into proximity with ubiquitination machinery. This molecule is most useful for enzymology, GTPase biology, nucleotide-binding assay development, affinity probe design, and exploratory ligand discovery rather than routine heterobifunctional PROTAC construction.

Guanosine 5'-diphosphate

Structure of 146-91-8

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Ligand for Target Protein
Molecular Formula
C10H15N5O11P2
Molecular Weight
443.20
Related CAS
7415-69-2 (disodium salt) 79441-34-2 (triammonium salt)
Appearance
Solid

* For research and manufacturing use only. Not for human or clinical use.

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Purity
≥95% by HPLC
Solubility
Soluble in Water (50 mg/mL)
Appearance
Solid
Storage
Store at -20°C
IUPACName
[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Synonyms
GDP; ((2R,3S,4R,5R)-5-(2-Amino-6-oxo-1H-purin-9(6H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl trihydrogen diphosphate; Guanosine diphosphate; 2-amino-9-{5-O-[hydroxy(phosphonooxy)phosphoryl]-β-D-ribofuranosyl}-9H-purin-6-ol; Guanosine 5'-(trihydrogen diphosphate)
Boiling Point
961.0 °C at 760 mmHg
Density
2.63±0.10 g/cm3
InChI Key
QGWNDRXFNXRZMB-UUOKFMHZSA-N
InChI
InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
SMILES
C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Mechanism

Mechanism of Action: Guanosine 5'-diphosphate is useful for customers studying GTPase-dependent regulation of intracellular trafficking and protein turnover. As a key nucleotide state in GTPase cycling, it can support analysis of autophagy, lysosomal transport, vesicle dynamics, and degradation-linked signaling pathways.

Applications

• Nucleotide-Based E3 Recruitment: Guanosine 5'-diphosphate can be used as a functional ligand element in PROTAC designs that aim to engage nucleotide-binding or related recognition pockets on target proteins, enabling proximity-driven ubiquitination. In targeted protein degradation workflows, such moieties may support rational placement of the linker to promote efficient ternary complex formation and subsequent proteasomal turnover.

• Proximity-Driven Degradation Studies: This nucleotide scaffold may be incorporated into PROTAC constructs to systematically test how binding orientation and linker geometry influence formation of an E3 ligase–target–PROTAC ternary complex. Researchers can evaluate degradation kinetics, dose–response behavior, and dependence on ubiquitination machinery to determine whether Guanosine 5'-diphosphate–anchored binding enhances selective depletion.

• Biochemical Mechanism Probing: Guanosine 5'-diphosphate–based PROTACs can be applied to dissect degradation mechanisms in nucleotide-regulated protein systems. By comparing degradation outcomes across mutants that alter nucleotide binding or conformational states, investigators can infer whether ternary complex stability and receptor engagement are the dominant determinants of ubiquitin-mediated clearance.

• Structure-Guided PROTAC Optimization: The diphosphate functionality offers handles for designing linker attachment strategies that preserve key electrostatic interactions while tuning spatial reach. In PROTAC optimization, researchers can use structure-guided modeling and iterative synthesis to refine binding affinity, ternary complex residence, and degradation potency, targeting improved selectivity over closely related nucleotide-binding proteins.

1. Direct incorporation of guanosine 5'-diphosphate into microtubules without guanosine 5'-triphosphate hydrolysis
E Hamel, J K Batra, C M Lin Biochemistry. 1986 Nov 4;25(22):7054-62.doi: 10.1021/bi00370a045.
Using highly purified calf brain tubulin bearing [8-14C]guanosine 5'-diphosphate (GDP) in the exchangeable nucleotide site and heat-treated microtubule-associated proteins (both components containing negligible amounts of nucleoside diphosphate kinase and nonspecific phosphatase activities), we have found that a significant proportion of exchangeable-site GDP in microtubules can be incorporated directly during guanosine 5'-triphosphate (GTP) dependent polymerization of tubulin, without an initial exchange of GDP for GTP and subsequent GTP hydrolysis during assembly. The precise amount of GDP incorporated directly into microtubules is highly dependent on specific reaction conditions, being favored by high tubulin concentrations, low GTP and Mg2+ concentrations, and exogenous GDP in the reaction mixture. Minimum effects were observed with changes in reaction pH or temperature, changes in concentration of microtubule-associated proteins, alteration of the sulfonate buffer, or the presence of a calcium chelator in the reaction mixture. Under conditions most favorable for direct GDP incorporation, about one-third of the GDP in microtubules is incorporated directly (without GTP hydrolysis) and two-thirds is incorporated hydrolytically (as a consequence of GTP hydrolysis). Direct incorporation of GDP occurs in a constant proportion throughout elongation, and the amount of direct incorporation probably reflects the rapid equilibration of GDP and GTP at the exchangeable site that occurs before the onset of assembly.
2. Combinatorial Modular Pathway Engineering for Guanosine 5'-Diphosphate-l-fucose Production in Recombinant Escherichia coli
Li Wan, Yingying Zhu, Wen Li, Wenli Zhang, Wanmeng Mu J Agric Food Chem. 2020 May 20;68(20):5668-5675.doi: 10.1021/acs.jafc.0c01064.Epub 2020 May 6.
Guanosine 5'-diphosphate (GDP)-l-fucose is an important nucleotide sugar involved in the synthesis of fucosylated oligosaccharides, such as fucosylated human milk oligosaccharides, which play important roles in physiological and pathological processes. Here, a combinatorial modular pathway engineering strategy was implemented to efficiently increase the intracellular titers of GDP-l-fucose in engineered Escherichia coli. The de novo GDP-l-fucose synthesis pathway was partitioned into two modules and fine-tuned at both transcriptional and translational levels, which remarkably improved the GDP-l-fucose production. In addition, the gene encoding the UDP-glucose lipid carrier transferase (WcaJ) was inactivated to eliminate the competing metabolite pathway from GDP-l-fucose to colanic acid. Furthermore, cofactors were regenerated to promote biocatalysis. Taken together, the final engineered strain EWL37, which could achieve a titer of 18.33 mg/L in shake-flask cultivation, showed 106.21 mg/L intracellular GDP-l-fucose accumulation and a DCW-specific GDP-l-fucose content of 4.28 mg/g through fed-batch cultivation. In general, this study demonstrated that the utilization of combinatorial modular pathway engineering significantly improved the de novo synthesis of GDP-l-fucose in engineered E. coli.
3. Guanosine diphosphate activates an adenosine 5'-triphosphate-sensitive K+ channel in the rabbit portal vein
S Kajioka, K Kitamura, H Kuriyama J Physiol. 1991 Dec;444:397-418.doi: 10.1113/jphysiol.1991.sp018885.
1. Properties of the pinacidil-sensitive K+ channel in the smooth muscle of the rabbit portal vein were investigated using cell-attached and inside- and outside-out patch clamp techniques. 2. In the cell-attached patch configuration, a K+ channel with a unitary conductance of 150 pS could be recorded when physiological salt solution (PSS) was in the pipette and high-K+ solution was in the bath. Tetraethylammonium (TEA; less than 1 mM) and charybdotoxin (CTX; greater than 50 nM) inhibited the 150 pS K+ channel from the outside of the membrane. This channel was activated by an increase in the concentrations of intracellular Ca2+ but not by pinacidil (less than or equal to 500 microM). 3. In the cell-attached patch configuration, bath application of pinacidil (greater than 3 microM) activated a K+ channel (ATP-sensitive K+ channel) with a unitary conductance of 15 pS and the enhancing action of pinacidil was blocked by glibenclamide. However, in the cell-free patch configuration, pinacidil (100 microM) failed to open the 15 pS K+ channel. With pinacidil in the pipette, the 15 pS K+ channel was completely inactivated within 5 s of the excision of the membrane. Opening of the 15 pS K+ channel also disappeared after saponin treatment (50 micrograms/ml). 4. In the cell-free patch configuration, application of guanosine 5'-diphosphate (GDP; greater than 100 microM) re-activated the inactivated 15 pS K+ channel only when pinacidil was present either in the pipette or bath. GDP increased the mean open time and open probability of the 15 pS K+ channel in a concentration-dependent manner. Simultaneous application of MgCl2 (less than or equal to 1 mM) with GDP did not modify the GDP-induced activation. Neither GDP nor GTP (1 mM) had any effect on the 150 pS K+ channel. 5. Guanosine 5'-triphosphate (GTP; 1 mM) activated the 15 pS K+ channel to a lesser extent that did GDP. Other guanine nucleotides (guanosine 5'-monophosphate, GMP, 1 mM; guanosine 5'-O-(3-thiotriphosphate), GTP gamma S, 100 microM; and guanosine 5'-O-(2-thiodiphosphate), GDP beta S, 1 mM) failed to activate the 15 pS K+ channel. However, GDP beta S, but not GMP or GTP gamma S, inhibited this channel when it was activated by 1 mM-GDP. 6. In the presence of pinacidil, adenosine 5'-triphosphate (ATP; greater than or equal to 10 microM) inhibited the ATP-sensitive K+ channel when it was activated by 1 mM-GDP.(ABSTRACT TRUNCATED AT 400 WORDS)

Structure: The structure of Guanosine 5'-diphosphate is characterized by primary or secondary amine/basic nitrogen centers; phenol or alcohol functionality. These features provide defined hydrogen-bonding, hydrophobic, and steric elements that can support affinity retention while enabling analogue-based linker-vector selection.

Reactivity: The amine/basic nitrogen-containing motif can be evaluated for acylation, sulfonylation, alkylation, or carbamate/urea linker installation when that vector is solvent exposed. For PROTAC construction, the POI ligand can be paired with CRBN ligands such as thalidomide, pomalidomide, or lenalidomide analogues, VHL ligands such as VH032 derivatives, or less common IAP/MDM2/cIAP-recruiting ligands, with alkyl, PEG, piperazine, triazole, or amide linkers screened for ternary-complex formation. In practice, incorporation into PROTACs should begin from derivatives that preserve the reported binding pharmacophore, followed by systematic variation of linker length, polarity, rigidity, and exit-vector geometry to optimize target engagement, E3 recruitment, and cellular degradation readouts.

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It is commonly abbreviated as: C1V1 = C2V2

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Tip: Chemical formula is case sensitive. C22H30N4O c22h30n40
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