dRibose5P_dRibose5P – 2-Deoxy-D-ribose 5-phosphate dimer

Name
WID	dRibose5P_dRibose5P
Name	2-Deoxy-D-ribose 5-phosphate dimer
Traditional name	(3,5-dihydroxyoxolan-2-yl)methyl {5-hydroxy-2- [(phosphonatooxy)methyl]oxolan-3-yl} phosphate
IUPAC name	(3,5-dihydroxyoxolan-2-yl)methyl {5-hydroxy-2- [(phosphonatooxy)methyl]oxolan-3-yl} phosphate

Structure
Empirical formula (pH 7.5)	H₁₇C₁₀O₁₃P₂
SMILES (pH 7.5)	OC1CC(O)C(COP([O-])(=O)OC2CC(O)OC2COP([O-])([O-])=O)O1
Charge (pH 7.5)	-3
Is hydrophobic	False
Molecular weight (Da)	407.18
van der Waals volume (pH 7.5; Å³ molecule^‑1)	302.62
logP	-9.28
logD (pH 7.5)	-7.88

Function
Reaction participant	EcoD DNA restriction/modification, DNA restriction [c]: ATP + (2) dRibose5P_dRibose5P + (3) H2O ⇒ ADP + (4) DR5P + (3) H + PI DNA ligationi [c]: (2) DR5P + NAD ⇒ AMP + dRibose5P_dRibose5P + H + NMN 3'-apurinic/apyrimidinic lyase [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H MunI DNA restriction/modification, DNA restriction [c]: (2) dRibose5P_dRibose5P + (2) H2O ⇒ (4) DR5P + (2) H DNA ligation [c]: (2) DR5P + NAD ⇒ AMP + dRibose5P_dRibose5P + H + NMN ... 7 more Spontaneous abasic site strand break [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H 5'-deoxyribophosphodiesterase; exonuclease [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H Radiation (gamma-ray) induced strand break dRibose5P_dRibose5P[c] + gamma_radiation[e] + H2O[c] ⇒ (2) DR5P[c] + H[c] deoxyribose 5'-phosphate lyase [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H 5'-apurinic/apyrimidinic endonuclease [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H DNA incision [c]: ATP + (2) dRibose5P_dRibose5P + (3) H2O ⇒ ADP + (4) DR5P + (3) H + PI DNA recombination Holliday junction resolution [c]: (2) dRibose5P_dRibose5P + (2) H2O ⇒ (4) DR5P + (2) H

Metadata
Created	2012-10-01 15:06:55
Last updated	2012-10-01 15:12:04