Molecule image
Summary
| Full name | 5-methyldihydrouridine |
| Short name | m5D |
| New Nomenclature | 58U |
| RNAMods abbreviation | ρ |
| Enzymes | |
| Found in phylogeny | |
| Found in RNA | |
| SMILES | C3(OC(CO)C(O)C(O)3)N1CC(C)C(=O)NC1(=O) |
| SMILES (no stereochemical information) | 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.
3D Molecule representation
Download [.mol file for m5D]
Chemical groups contained
| Type | Subtype |
|---|---|
| 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: Oct. 6, 2017