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4-Amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)-2-oxolanyl]-2-pyrimidinone

HCID 3461
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Basic informationOverviewNames & identifiersPropertiesSafety & regulationChemistry & industryRelated reactionsCompound notes
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Basic information

CAS
95058-81-4
Standard SMILES
Nc1ccn(C2OC(CO)C(O)C2(F)F)c(=O)n1
InChIKey
SDUQYLNIPVEERB-UHFFFAOYSA-N
Molecular formula
C9H11F2N3O4
Average molar mass
263.2 g/mol
Monoisotopic mass
263.07176216

Overview

4-amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)-2-oxolanyl]-2-pyrimidinone is a pyrimidine 2'-deoxyribonucleoside.

Names & identifiers

Preferred name
4-Amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)-2-oxolanyl]-2-pyrimidinone
IUPAC
4-amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
English name
Gemcitabine
Molecular formula
C9H11F2N3O4
Molecular weight
263.2

Names & synonyms

103882-85-54-amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one701937-51-14-amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)-2-oxolanyl]-2-pyrimidinone4-amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one3'-Epi Gemcitabine (Gemcitabine Impurity)GemctitabineC9H11F2N3O4Neuro_000239SCHEMBL949604-amino-1-(2-deoxy-2,2-difluoropentofuranosyl)pyrimidin-2(1H)-oneCHEMBL264883
Show more names
GeMcitabingemicitabineGEMCITABINE HCL USP4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2(1H)-one4-Amino-1-((2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-oneZefeiGemcelGemLipT11BaseLY-18011
orb1301102CHEBI:93766SDUQYLNIPVEERB-UHFFFAOYSA-NHMS3655E04HMS5079H162;-Deoxy-2',2'-difluorocytidineEBC-70048NSC750927

Properties

Computed structural properties

XLogP
-1.5
Topological polar surface area
108 Ų
Hydrogen bond donors
3
Hydrogen bond acceptors
6
Rotatable bonds
2
Heavy atoms
18
Formal charge
0
Complexity
426

Experimental & physicochemical properties

DrugsPharmaceuticals

Physicochemical properties

Melting point
168 · 168,64 C
alpha
365 · 365 +425.36°; D +71.51°
Boiling point
482.7 · 482.7±55.0 °C(Predicted)
Density
1.84 · 1.84±0.1 g/cm3(Predicted)
storage temp.
-20 °C · Keep in dark place,Sealed in dry,Store in freezer, under -20°C
solubility
Methanol (Slightly), Water (Slightly, Heated)
pka
11.65 · 11.65±0.70(Predicted)
form
Solid
color
White to Off-White
InChI
InChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1
InChIKey
SDUQYLNIPVEERB-QPPQHZFASA-N
SMILES
OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)[C@](F)(F)[C@@H]1O

Safety & regulation

Safety information is for reference only and does not replace the supplier’s Safety Data Sheet (SDS), applicable regulations, or professional assessment.

Safety data

hs_code
29349990
Toxicity
LD10 i.v. in rats: 200 mg/m2 (Abbruzzese)
risk_code
21-36/38-46-62-63
Signal word
Danger
Symbol(GHS)
GHS07
hazard_code
Xn,Xi
safety_code
25-26-36/37-53
Hazard statements
H312-H315-H319-H340-H361
Precautionary statements
P280-P308+P313
Hazardous Substances Data
95058-81-4(Hazardous Substances Data)

Chemistry & industry

Applications · 5 items

DescriptionGemcitabine (2’,2’-difluorodeoxycytidine; dFdCyd) is a novel deoxycytidine analogue with both structural and metabolic similarities to cytarabine. It has a broad spectrum of antitumor activity in preclinical murine leukemia and solid tumor models. This drug requires intracellular phosphorylation that results in the accumulation of difluorodeoxycytidine triphosphate (dFdCTP). The dFdCTP competes with deoxycytidine triphosphate (dCTP) for incorporation into DNA, which in turn inhibits DNA synthesis and terminates DNA chain elongation. In addition, this drug reduces intracellular deoxynucleoside triphosphate pools, presumably through the inhibition of ribonucleotide reductase. Gemcitabine is used alone or with other treatments/medications to treat certain types of cancer (including breast cancer, non-small cell lung cancer, ovarian cancer, pancreatic cancer, bladder cancer, bone cancer, Ewing’s sarcoma, mesenchymal chondrosarcoma osteosarcoma, dedifferentiated chondrosarcoma, head and neck cancers-cancer of the nasopharynx, hepatobiliary cancers including gallbladder cancer, Hodgkin lymphoma, kidney cancer, malignant pleural mesothelioma, non Hodgkin lymphoma, non-melanoma skin cancer – dermatofibrosarcoma protuberans (DFSP), occult primary, small cell lung cancer, soft tissue sarcoma, testicular cancer, thymic malignancies, uterine malignancies). It is a chemotherapy drug that works by slowing or stopping the growth of cancer cells. One commercial product of gemcitabine is Gemzar, which is supplied in a sterile form for intravenous use only.

DescriptionGemcitabine is an anticancer nucleoside analog that inhibits the growth of HL-60 promyelocytic leukemia cells with an LC50 value of 40 nM. It inhibits the growth of MX-1 mammary, CX-1, HC-1, GC3, and VRC5 colon, LX-1, Calu-6, and NCI-H460 lung, and HS766T, PaCa-2, PANC-1, and BxPC-3 pancreatic cancer tumors in mouse xenograft models (45-93% inhibition). Gemcitabine is a prodrug that is metabolized to a diphosphate and triphosphate form in cells. The triphosphate form is incorporated into DNA which induces masked chain termination and cell death. By specifically inhibiting growth arrest and DNA damage inducible protein 45 a (Gadd45a), a key mediator of active DNA demethylation, gemcitabine, at concentrations ranging from 34 to 134 nM, inhibits repair-mediated DNA demethylation in a methylation-sensitive reporter assay. Gemcitabine also has broad antiretroviral activity, decreasing MuLV cell infectivity, a murine AIDS model, in cell culture (EC50 = ~1.5 nM) and inhibits the progression of murine AIDS in vivo at a dose of 1-2 mg/kg per day.

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Related reactions

4 records
New reaction record
HRID 140480 reaction equation
HRID 140480As reactantTraining data from https://doi.org/10.1039/C8SC04228D (9/10)
HRID 814931 reaction equation
HRID 814931As reactantTest data from https://doi.org/10.1039/C8SC04228D
HRID 935863 reaction equation
HRID 935863As reactantValidation data from https://doi.org/10.1039/C8SC04228D
HRID 2151093 reaction equation
HRID 2151093As reactantTraining data from https://doi.org/10.1039/C8SC04228D (4/10)

Compound notes

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On this pageBasic informationOverviewNames & identifiersPropertiesSafety & regulationChemistry & industryRelated reactionsCompound notes

Database identifiers

CAS
95058-81-4
PubChem CID
3461
ChEMBL
CHEMBL264883
ChEBI
CHEBI:93766
Nikkaji
J3.629.991F
CAS DataBase Reference
95058 · 95058-81-4(CAS DataBase Reference)
EWG's Food Scores
1 · 1
FDA UNII
76 N6SBZ8R · B76N6SBZ8R
ATC code
1 BC05 · L01BC05
Protein binding
Negligible
Excreted unchanged in urine
10 % · <10%
Volume of distribution
12.4 Litres/m2 · 12.4 Litres/m2 (women); 17.5 Litres/ m2 (men)
Biological half-life
42 · 42-94 minutes / -
Symbol(GHS)
7 · GHS07
Signal word
Danger
Hazard statements
312 · H312-H315-H319-H340-H361
Precautionary statements
280 · P280-P308+P313
Hazard Codes
Xn,Xi
Risk Statements
21 · 21-36/38-46-62-63
Safety Statements
25 · 25-26-36/37-53
HS Code
29349990 · 29349990
Hazardous Substances Data
95058 · 95058-81-4(Hazardous Substances Data)
Toxicity
10 i.v · LD10 i.v. in rats: 200 mg/m2 (Abbruzzese)

UsesGemcitabine is used for breast cancer treatment. First-line treatment for locally advanced pancreatic cancer.

UsesGemcitabine(Gemzar) belongs to the group of medicines called antimetabolites. It is used alone or in combination with other medicines to treat cancer of the breast, ovary, pancreas, and lung. Gemcitabine interferes with the growth of cancer cells, which a

General DescriptionThe drug is available as the hydrochloride salt in 200- and1,000-mg lyophilized single-dose vials for IV use.Gemcitabine is used to treat bladder cancer, breast cancer,pancreatic cancer, and NSCLC. Gemcitabine is a potent radiosensitizer,and it increases the cytotoxicity of cisplatin.The mechanism of action of this fluorine-substituted deoxycytidineanalog involves inhibition of DNA synthesis andfunction via DNA chain termination. The triphosphatemetabolite is incorporated into DNA inhibiting severalDNA polymerases and incorporated into RNA inhibitingproper function of mRNA. Resistance can occur because ofdecreased expression of the activation enzyme deoxycytidinekinase or decreased drug transport as well as increasedexpression of catabolic enzymes. Drug oral bioavailabilityis low because of deamination within the GI tract, and thedrug does not cross the blood-brain barrier. Metabolism bydeamination to 2', 2'-difluorouridine (dFdU) is extensive.Drug toxicity includes myelosuppression, fever, malaise,chills, headache, myalgias, nausea, and vomiting.

Upstream & downstream products

Upstream raw materials

Dimethyl sulfateAmmonium sulfatePyridineSodium periodateHydrogenMethyl 4,5-dimethoxy-2-nitrobenzoateOzoneDimethyl sulfideTriethylamineN4-AcetylcytosineN,N-DiisopropylethylamineHydrogen peroxideTitanium tetraisopropanolatePalladium hydroxidePhenylselenolTrimethylsilyl trifluoromethanesulfonate

Downstream products

Acelarin
Additional notes · 1 item

DefinitionChEBI: Gemcitabine is a 2'-deoxycytidine having geminal fluoro substituents in the 2'-position. An inhibitor of ribonucleotide reductase, gemcitabine is used in the treatment of various carcinomas, particularly non-small cell lung cancer, pancreatic cancer, bladder cancer and breast cancer. It has a role as a photosensitizing agent, a DNA synthesis inhibitor, a prodrug, an EC 1.17.4.1 (ribonucleoside-diphosphate reductase) inhibitor, an environmental contaminant, a xenobiotic, a radiosensitizing agent, an antineoplastic agent, an antimetabolite, an antiviral drug and an immunosuppressive agent. It is an organofluorine compound and a pyrimidine 2'-deoxyribonucleoside.