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- ChemComp-D4M: [(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DI... -

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Basic information

EntryDatabase: PDB chemical components / ID: D4M
NameName: [(5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl dihydrogen phosphate
Synonyms: 2',3'-DIDEOXY-2',3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE; 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-MONOPHOSPHATE

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Chemical information

Composition
Formula: C10H13N2O7P / Number of atoms: 33 / Formula weight: 304.193 / Formal charge: 0
Others

1z4q

DT

Type: DNA LINKING / PDB classification: ATOMN / One letter code: T / Three letter code: D4M / Model coordinates PDB-ID: 1Z4Q / Parent comp.: DT
History
Create componentMay 10, 2005
Modify descriptorJun 4, 2011
Modify synonymsMay 27, 2020
External linksUniChem / ChemSpider / 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 10.04O=C1NC(=O)N(C=C1C)C2OC(C=C2)COP(=O)(O)O
CACTVS 3.341CC1=CN([CH]2O[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2C=CC(O2)COP(=O)(O)O

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SMILES CANONICAL

CACTVS 3.341CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)C=C2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C=C[C@H](O2)COP(=O)(O)O

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InChI

InChI 1.03InChI=1S/C10H13N2O7P/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(19-8)5-18-20(15,16)17/h2-4,7-8H,5H2,1H3,(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1

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InChIKey

InChI 1.03XLPGURCDSRIXFL-JGVFFNPUSA-N

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SYSTEMATIC NAME

ACDLabs 10.04[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl dihydrogen phosphate
OpenEye OEToolkits 1.5.0[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-2-yl]methyl dihydrogen phosphate

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PDB entries

Showing all 3 items

PDB-1z4q:
Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)

PDB-6uu3:
E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Old" crystal soaked with GTP, ATP, CTP, and ddTTP for 30 minutes)

PDB-6wpf:
Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and d4T

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