Molecule image

m5D

Summary

Full name5-methyldihydrouridine
Short namem5D
New Nomenclature58U
RNAMods abbreviationρ
Enzymes
Found in phylogeny
Found in RNA
SMILESC3(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 formulaC10O6N2H16
Monoisotopic mass260.1008
Average mass260.2473
[M+H]+261.1086
Product ions129
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

TypeSubtype
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: Oct. 6, 2017

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