Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

5HC : Summary

Code

5HC

One-letter code

C

Molecule name

2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H16 N3 O8 P

Formal charge

0

Molecular weight

337.223 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)CC2O
SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1CO)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
SMILES OpenEye OEToolkits 1.7.6 C1C(C(OC1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1CO)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
Canonical SMILES OpenEye OEToolkits 1.7.6 C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H16N3O8P/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(21-8)4-20-22(17,18)19/h2,6-8,14-15H,1,3-4H2,(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1

IUPAC InChI key

BTIWPBKNTZFNRI-XLPZGREQSA-N
5HC

wwPDB Information

Atom count

38 (22 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

2012-08-22

Last modified at

2013-01-11

Status

Released

Obsoleted

Not Assigned