Modification Summary

5-methyldihydrouridine

[show modification pathway]
m5D

Summary

Full name5-methyldihydrouridine
Short namem5D
New Nomenclature58U
RNAMods abbreviationρ
HTML abbreviationρ
Enzymes
Found in phylogeny
Found in RNA
SMILES codeC3(OC(CO)C(O)C(O)3)N1CC(C)C(=O)NC1(=O)

LC-MS Informations

Sum formulaC10O6N2H16
Monoisotopic mass260.100836
Average mass260.247258
HRMS mass260.100287
Normalized LC elution time * not available
LC elution order/characteristics not available
Mass transition not available

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

Download [.mol file for m5D]

Chemical groups contained

methyl groupmethyl at aliphatic C
ring modificationpartial saturation

Reactions producing 5-methyldihydrouridine

Name
D:m5D

Occurrence in PDB structures

PDB-ID chain residue
176d A TPN /5
1ac3 A TSP /6
1d7z A 6HT /2
1d7z A 6HT /4
1dau A 6CT /7
1dau A 6CT /8
1dau B 6CT /19
1dau B 6CT /20
1dpl A T23 /6
1dpl B T23 /16
1ec4 A 6HT /5
1ec4 A 6HT /6
1ec4 A 6HT /7
1ec4 A 6HT /8
1ec4 B 6HT /17
1ec4 B 6HT /18
1ec4 B 6HT /19
1ec4 B 6HT /20
1ei4 A TLC /7
1ei4 A TLC /8
1ei4 B TLC /19
1ei4 B TLC /20
1ejz B 6HT /12
1eo3 C TSP /6
1eo3 D TSP /6
1eo4 C TSP /6
1eo4 D TSP /6
1eon C TSP /6
1eon D TSP /6
1gv6 A ATL /2
1gv6 A ATL /5
1gv6 A ATL /6
1gv6 A ATL /8
1h0q A TLN /2
1h0q A TLN /5
1h0q A TLN /7
1hhw A TLN /5
1hzs A TPN /4
1hzs B TPN /12
1hzs C TPN /20
1hzs D TPN /28
1i0f A 127 /6
1i0f B 127 /16
1i0g A 125 /6
1i0g B 125 /16
1i0j A MEP /6
1i0j B MEP /16
1i0k A 126 /6
1i0k B 126 /16
1i0m A 125 /6
1i0m B 125 /16
1i0n A 126 /6
1i0n B 126 /16
1i0o A MEP /6
1i0o B MEP /16
1i0p A 126 /6
1i0p B 126 /16
1i0q A 126 /6
1i0q B 126 /16
1i5w A TLN /6
1i5w B TLN /16
1mlx B SMT /116
1nn0 2DT /301
1nn1 2DT /301
1nn3 2DT /301
1nn5 2DT /301
1nr8 B TPN /2
1nr8 B T66 /6
1nr8 B TPN /10
1nzg A 3ME /6
1nzg B 3ME /16
1oci A TLB /5
1okf A ATL /2
1okf A ATL /5
1okf A ATL /7
1pdt B TPN /11
1pdt B TPN /13
1pdt B TPN /15
1pnn A TPN /2
1pnn A TPN /4
1pnn A TPN /7
1pnn A TPN /8
1pnn A TPN /17
1pnn A TPN /18
1pnn A TPN /20
1pnn A TPN /21
1pnn A TPN /23
1pnn C TPN /2
1pnn C TPN /4
1pnn C TPN /7
1pnn C TPN /8
1pnn C TPN /17
1pnn C TPN /18
1pnn C TPN /20
1pnn C TPN /21
1pnn C TPN /23
1pup A TPN /3
1pup B TPN /10
1qpy A TP1 /3
1qpy B TP1 /3
1qpy C TP1 /3
1qpy D TP1 /3
1qpy E TP1 /3
1qpy F TP1 /3
1qpy G TP1 /3
1qpy H TP1 /3
1qtm B 2DT /112
1r3g A GMU /6
1r3g B GMU /16
1rru A TPN /3
1rru B TPN /11
1s9l A TLN /1
1s9l A TLN /5
1s9l B TLN /6
1s9l B TLN /10
1s9l C TLN /11
1s9l C TLN /15
1s9l D TLN /16
1sks P 2DT /21
1skw P 2DT /21
1sl0 P 2DT /21
1sl0 Q 2DT /21
1t8e C 2DT /1022
1tk8 D3T /823
1tkd D3T /823
1ttt D 5MU /54
1u01 A HDP /4
1wv5 A 2BT /6
1wv5 B 2BT /16
1x9m C 2DT /22
1x9s P 2DT /22
1x9w C 2DT /22
1xj9 A TPN /106
1xj9 A TPN /110
1xj9 B TPN /206
1xj9 B TPN /210
1xsn P 2DT /6
1xsn D3T /438
1xux A NMS /6
1xux B NMS /106
1xux C NMS /206
1xux D NMS /306
1y7f A 2NT /6
1y7f B 2NT /16
1y84 A EIT /6
1y84 B EIT /16
1y86 A 125 /6
1y86 B 125 /16
1y8l A TFE /6
1y8l B TFE /16
1y8v A P2T /6
1y8v B P2T /16
1y9f A 2AT /6
1y9f B 2AT /16
1y9s A 2GT /6
1y9s B 2GT /16
1yb9 A 2OT /6
1yb9 B 2OT /16
1ybc A BOE /6
1ybc B BOE /16
233d A +T /7
233d A +T /8
233d B +T /19
233d B +T /20
290d A +T /7
290d A +T /8
290d B +T /19
290d B +T /20
291d A +T /7
291d A +T /8
291d B +T /19
291d B +T /20
2ajq P 2DT /822
2ajq X 2DT /922
2bj6 A 6HT /4
2bj6 A 6HT /7
2bj6 B 6HT /4
2bj6 B 6HT /7
2bj6 C 6HT /4
2bj6 C 6HT /7
2bj6 D 6HT /4
2bj6 D 6HT /7
363d A +T /7
363d A +T /8
363d B +T /19
363d B +T /20
363d C +T /107
363d C +T /108
363d D +T /119
363d D +T /120
363d E +T /207
363d E +T /208
363d F +T /219
363d F +T /220
3bdp P 2DT /16
411d A +T /6
411d B +T /16
412d A +T /6
412d B +T /16
481d A 6HT /2
481d A 6HT /4
8ico A AZT /338

Last modification of this entry: 2013-05-10 16:36:59.994425
Edited by a user: magda
Edited content: Kingdom/s added to a modification