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) |
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]
Type | Subtype |
---|---|
methyl group | methyl at aliphatic C |
ring modification | partial saturation |
Name |
---|
D:m5D |
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