Chemical Components in the PDB

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5MD : Summary

Code

5MD

One-letter code

N

Molecule name

2'-deoxy-1-methyl-pseudouridine

Synonyms

5-METHYL-2'-DEOXYPSEUDOURIDINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R)-1,4-anhydro-2-deoxy-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-erythro-pentitol
OpenEye OEToolkits 1.5.0 5-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione

Formula

C10 H14 N2 O5

Formal charge

0

Molecular weight

242.229 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N(C=C(C(=O)N1)C2OC(CO)C(O)C2)C
SMILES CACTVS 3.341 CN1C=C([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 CN1C=C(C(=O)NC1=O)C2CC(C(O2)CO)O
Canonical SMILES CACTVS 3.341 CN1C=C([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CN1C=C(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O

IUPAC InChI

InChI=1S/C10H14N2O5/c1-12-3-5(9(15)11-10(12)16)7-2-6(14)8(4-13)17-7/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1

IUPAC InChI key

AMDJRICBYOAHBZ-XLPZGREQSA-N
5MD

wwPDB Information

Atom count

31 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

DNA LINKING

Type code

HETAIN

Is modified

Yes

Standard parent

Not Assigned

Defined at

2000-07-26

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned