Chemical Components in the PDB

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DDN : Summary

Code

DDN

One-letter code

U

Molecule name

3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Synonyms

((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (4R)-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-[(4R)-4-hydroxy-2-oxo-3,4-dihydropyrimidin-1-yl]oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H15 N2 O8 P

Formal charge

0

Molecular weight

310.198 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1NC(O)C=CN1C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C[CH](O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=CC(NC2=O)O)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C[C@@H](O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=C[C@H](NC2=O)O)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-8,12-13H,3-4H2,(H,10,14)(H2,15,16,17)/t5-,6+,7+,8+/m0/s1

IUPAC InChI key

ILSIYJVILUIVPM-LXGUWJNJSA-N
DDN

wwPDB Information

Atom count

35 (20 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

2004-12-14

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned