Chemical Components in the PDB

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5HM : Summary

Code

5HM

One-letter code

C

Molecule name

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

Synonyms

5-hydroxymethylcytidine 5'-monophosphate

Systematic names

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

Formula

C10 H16 N3 O9 P

Formal charge

0

Molecular weight

353.223 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)C(O)C2O
SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1CO)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.7.6 C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)CO
Canonical SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1CO)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)CO

IUPAC InChI

InChI=1S/C10H16N3O9P/c11-8-4(2-14)1-13(10(17)12-8)9-7(16)6(15)5(22-9)3-21-23(18,19)20/h1,5-7,9,14-16H,2-3H2,(H2,11,12,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1

IUPAC InChI key

KPUOHXMVCZBWQC-JXOAFFINSA-N
5HM

wwPDB Information

Atom count

39 (23 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

C

Defined at

2014-01-22

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned