Chemical Components in the PDB

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NDN : Summary

Code

NDN

One-letter code

U

Molecule name

2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-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

Formula

C9 H12 N3 O10 P

Formal charge

0

Molecular weight

353.179 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 [O-][N+](=O)C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=C(C(=O)NC2=O)[N+](=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(=O)NC2=O)[N+]([O-])=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O

IUPAC InChI

InChI=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

IUPAC InChI key

LVLPVLNNXRTCHP-RRKCRQDMSA-N
NDN

wwPDB Information

Atom count

35 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

2007-11-07

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned