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- ChemComp-NDN: 2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE) -

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Basic information

EntryDatabase: PDB chemical components / ID: NDN
NameName: 2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)
Synonyms: [(2R,3S,5R)-3-HYDROXY-5-(5-NITRO-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE

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Chemical information

Composition
Formula: C9H12N3O10P / Number of atoms: 35 / Formula weight: 353.179 / Formal charge: 0
Others

3b5b

DU

Type: DNA LINKING / PDB classification: ATOMN / One letter code: U / Three letter code: NDN / Ideal coordinates details: Corina / Model coordinates PDB-ID: 3B5B / Parent comp.: DU
History
Create componentNov 7, 2007
Modify descriptorJun 4, 2011
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / BindingDB / Brenda / ChEMBL / CompTox / PubChem / SureChEMBL / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

ACDLabs 10.04[O-][N+](=O)C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O

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SMILES CANONICAL

CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O

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InChI

InChI 1.03InChI=1S/C9H12N3O10P/c13-5-1-7(22-6(5)3-21-23(18,19)20)11-2-4(12(16)17)8(14)10-9(11)15/h2,5-7,13H,1,3H2,(H,10,14,15)(H2,18,19,20)/t5-,6+,7+/m0/s1

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InChIKey

InChI 1.03LVLPVLNNXRTCHP-RRKCRQDMSA-N

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SYSTEMATIC NAME

ACDLabs 10.042'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0[(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

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PDB entries

Showing all 1 items

PDB-3b5b:
Crystal structure of the thymidylate synthase k48q

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