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UDP

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C9H14N2O12P2 · 404.16 g/mol

IUPAC name: [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate

Also called uridine diphosphate

Nucleic acid parts
Open in Athanor
The structure of UDP
Drawn from its SMILES with RDKit

Names and identifiers

IUPAC name
[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Synonyms
uridine diphosphate, URIDINE DIPHOSPHATE, uridine-5'-diphosphate
+ 36 more

Uridine Pyrophosphate, URIDINE_DIPHOSPHATE, 5G0F599A1Y, DTXSID001018933, [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate, Diphosphate, Uridine, Pyrophosphate, Uridine, ((2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl)methyl phosphono hydrogen phosphate, RefChem:901480, DTXCID501476946, Uridine 5'-diphosphate, Uridine 5'-(trihydrogen diphosphate), 5'-UDP, Uridine 5'-pyrophosphate, Uridine 5'-pyrophosphoric acid, ((2R,3S,4R,5R)-5-(2,4-Dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl trihydrogen diphosphate, CHEMBL130266, Uridine, 5'-(trihydrogen diphosphate), [({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid, EINECS 200-409-6, UNII-5G0F599A1Y, 1gww, 1gx4, 1o7o, bmse000266, Uridine 5'-pyrophosphorate, Uridine diphosphate (6CI), SCHEMBL4245, Lopac0_001205, Uridine pyrophosphate (7CI), GTPL1749, orb2278531, CHEBI:17659, BDBM50118239, BDBM50403871, URIDINE 5'-DIPHOSPHATE [MI]

Molecular formula
C9H14N2O12P2
Empirical formula
C9H14N2O12P2
Molecular weight
404.16 g/mol
Exact mass
404.00220
CAS number
58-98-0
PubChem CID
6031
Canonical SMILES
C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
Isomeric SMILES
C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)O)O)O
InChI
InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKey
XCCTYIAWTASOJW-XVFCMESISA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms
25
Rings
2
Aromatic rings
1
Fraction sp³ carbons (Fsp3)
0.56
H-bond donors
6
H-bond acceptors
9 computed here · PubChem 12
Rotatable bonds
6
TPSA (Ų)
217.8 computed here · PubChem 212
Formal charge
0
XLogP3
-4.7 PubChem
Complexity
675 PubChem
Stereocenters
4 defined, 1 undefinedCIP: C6: R · C8: R · P11: undefined · C19: S · C21: R
Double-bond geometry
None specified
Point group
C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

  • C26.75%
  • H3.49%
  • N6.93%
  • O47.50%
  • P15.33%

Isotope pattern

100%404.00211%405.0053.0%406.007407.010

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P
-2.62 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-0.48 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
4.1 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 404.16
  • log P ≤ 5 (Crippen): -2.62
  • H-bond donors ≤ 5: 6
  • H-bond acceptors ≤ 10: 9

Breaks 1 of the four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

No GHS hazard classification was found in the sources.

Safety data sheets on the supplier’s page: NewCan Biotech, Mcule, Chem-Space.com Database.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. [1]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
  2. [2]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
  3. [3]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
  4. [4]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
  5. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  6. ·Literature on PubChem

Data last updated 2026-10-14.