Modification Summary
5-methyldihydrouridine
[show modification pathway]
Summary
| Full name | 5-methyldihydrouridine |
| Short name | m5D |
| New Nomenclature | 58U |
| RNAMods abbreviation | ρ |
| HTML abbreviation | ρ |
| Enzymes | |
| Found in phylogeny | |
| Found in RNA | |
| SMILES code | C3(OC(CO)C(O)C(O)3)N1CC(C)C(=O)NC1(=O) |
LC-MS Information
| Sum formula | C10O6N2H16 |
| Monoisotopic mass | 260.1008 |
| Average mass | 260.2473 |
| [M+H]+ | 261.1086 |
| Product ions | 129 |
| Normalized LC elution time * | not available |
| LC elution order/characteristics | 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 group | methyl at aliphatic C |
| ring modification | partial 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
