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- ChemComp-3YN: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-... -

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Basic information

EntryDatabase: PDB chemical components / ID: 3YN
NameName: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl
Synonyms: TDP-4-keto-D-olivose

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Chemical information

Composition
Formula: C16H24N2O14P2 / Number of atoms: 58 / Formula weight: 530.314 / Formal charge: 0
Others

4rvh

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: 3YN / Ideal coordinates details: Corina / Model coordinates PDB-ID: 4RVH
History
Create componentDec 10, 2014
Initial releaseJan 28, 2015
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / Brenda / ChEBI / KEGG_Ligand / Metabolights / Nikkaji / PubChem / ZINC / 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 12.01O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(=O)C(O)C3)C)O)O)C
CACTVS 3.385C[CH]1O[CH](C[CH](O)C1=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O
OpenEye OEToolkits 1.7.6CC1C(=O)C(CC(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O

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SMILES CANONICAL

CACTVS 3.385C[C@H]1O[C@@H](C[C@@H](O)C1=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O
OpenEye OEToolkits 1.7.6C[C@@H]1C(=O)[C@@H](C[C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O

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InChI

InChI 1.03InChI=1S/C16H24N2O14P2/c1-7-5-18(16(23)17-15(7)22)12-3-9(19)11(30-12)6-28-33(24,25)32-34(26,27)31-13-4-10(20)14(21)8(2)29-13/h5,8-13,19-20H,3-4,6H2,1-2H3,(H,24,25)(H,26,27)(H,17,22,23)/t8-,9+,10-,11-,12-,13-/m1/s1

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InChIKey

InChI 1.03AONILRCSLAIOQE-LREJFELKSA-N

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SYSTEMATIC NAME

ACDLabs 12.01[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.7.6[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,4R,6R)-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-2-yl] hydrogen phosphate

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PDB entries

Showing all 1 items

PDB-4rvh:
Crystal structure of MtmC in complex with SAH and TDP-4-keto-D-olivose

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