Chemical Components in the PDB

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XRF : Summary

Code

XRF

One-letter code

X

Molecule name

1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 2.0.7 [[(2~{S},3~{R},5~{S})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Formula

C10 H17 N2 O14 P3

Formal charge

0

Molecular weight

482.168 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(CC1O)N1C=C(C)C(=O)NC1=O
SMILES CACTVS 3.385 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 2.0.7 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m1/s1

IUPAC InChI key

NHVNXKFIZYSCEB-CSMHCCOUSA-N
XRF

wwPDB Information

Atom count

46 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-03-09

Last modified at

2022-02-18

Status

Released

Obsoleted

Not Assigned