NAV

2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate

Identification

Generic Name
2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate
DrugBank Accession Number
DB03961
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 278.0909
Monoisotopic: 277.995655006
Chemical Formula
C5H12O9P2
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
U2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseNot AvailableShigella flexneri
Absorption

Not Available

Volume of distribution

Not Available

Protein binding

Not Available

Metabolism
Not Available
Route of elimination

Not Available

Half-life

Not Available

Clearance

Not Available

Adverse Effects
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Toxicity

Not Available

Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Not Available
Food Interactions
Not Available

Categories

Drug Categories
Not Available
Chemical TaxonomyProvided by Classyfire
Description
This compound belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
Kingdom
Organic compounds
Super Class
Organic oxygen compounds
Class
Organic oxoanionic compounds
Sub Class
Organic pyrophosphates
Direct Parent
Organic pyrophosphates
Alternative Parents
Organic phosphoric acids and derivatives / Secondary alcohols / Polyols / Oxacyclic compounds / Primary alcohols / Organic oxides / Hydrocarbon derivatives
Substituents
Alcohol / Aliphatic heteromonocyclic compound / Hydrocarbon derivative / Organic oxide / Organic phosphoric acid derivative / Organic pyrophosphate / Organoheterocyclic compound / Organooxygen compound / Oxacycle / Polyol
Molecular Framework
Aliphatic heteromonocyclic compounds
External Descriptors
tetritol phosphate (CHEBI:18425)
Affected organisms
Not Available

Chemical Identifiers

UNII
Not Available
CAS number
Not Available
InChI Key
SFRQRNJMIIUYDI-UHNVWZDZSA-N
InChI
InChI=1S/C5H12O9P2/c1-5(3-6)4(7)2-12-15(8,9)14-16(10,11)13-5/h4,6-7H,2-3H2,1H3,(H,8,9)(H,10,11)/t4-,5+/m1/s1
IUPAC Name
(6S,7R)-2,4,7-trihydroxy-6-(hydroxymethyl)-6-methyl-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-dione
SMILES
[H][C@@]1(O)COP(O)(=O)OP(O)(=O)O[C@@]1(C)CO

References

General References
Not Available
KEGG Compound
C11453
PubChem Compound
126747
PubChem Substance
46507462
ChemSpider
112576
ChEBI
18425
ZINC
ZINC000008419115
PDBe Ligand
CDI
PDB Entries
1h48 / 1jy8 / 1knj / 4g9p / 4s38

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage Forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not Available
Predicted Properties
PropertyValueSource
Water Solubility21.4 mg/mLALOGPS
logP-0.81ALOGPS
logP-1.8Chemaxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.83Chemaxon
pKa (Strongest Basic)-3.1Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count6Chemaxon
Hydrogen Donor Count4Chemaxon
Polar Surface Area142.75 Å2Chemaxon
Rotatable Bond Count1Chemaxon
Refractivity49.08 m3·mol-1Chemaxon
Polarizability20.4 Å3Chemaxon
Number of Rings1Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption+0.7157
Blood Brain Barrier+0.894
Caco-2 permeable-0.6693
P-glycoprotein substrateSubstrate0.6102
P-glycoprotein inhibitor INon-inhibitor0.6868
P-glycoprotein inhibitor IINon-inhibitor0.9802
Renal organic cation transporterNon-inhibitor0.943
CYP450 2C9 substrateNon-substrate0.804
CYP450 2D6 substrateNon-substrate0.8198
CYP450 3A4 substrateNon-substrate0.5266
CYP450 1A2 substrateNon-inhibitor0.8566
CYP450 2C9 inhibitorNon-inhibitor0.8506
CYP450 2D6 inhibitorNon-inhibitor0.8985
CYP450 2C19 inhibitorNon-inhibitor0.8256
CYP450 3A4 inhibitorNon-inhibitor0.9277
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9803
Ames testNon AMES toxic0.664
CarcinogenicityNon-carcinogens0.8185
BiodegradationNot ready biodegradable0.9935
Rat acute toxicity2.3215 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.8235
hERG inhibition (predictor II)Non-inhibitor0.8521
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-03di-0290000000-2dff5f2bf53fe03d85e3
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0032-9610000000-c55922df81ce1a669b74
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-1090000000-3ed6b2a2eded85c9363d
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9670000000-b8796161ee6ca176c958
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0002-9000000000-5bbe1eda1a80a2a59226
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9150000000-8be74c8392108874911b
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-130.6009
predicted
DeepCCS 1.0 (2019)
[M+H]+134.25824
predicted
DeepCCS 1.0 (2019)
[M+Na]+142.64418
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Kind
Protein
Organism
Shigella flexneri
Pharmacological action
Unknown
General Function
Metal ion binding
Specific Function
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidy...
Gene Name
ispF
Uniprot ID
P62619
Uniprot Name
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Molecular Weight
16897.37 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52