ChemComp-DI0: Dirithromycin

Basic information

• Entry: Database: PDB chemical components / ID: DI0
• Name: Name: Dirithromycin; Synonyms: (1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethy
• Comment: antibiotic*YM

Chemical information

Composition

Formula: C₄₂H₇₈N₂O₁₄ / Number of atoms: 136 / Formula weight: 835.074 / Formal charge: 0

Others

6of1

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: DI0 / Ideal coordinates details: Corina / Model coordinates PDB-ID: 6OF1

History

Create component	Mar 29, 2019
Initial release	Apr 17, 2019
Modify synonyms	Jun 5, 2020

• External links: UniChem / ChemSpider / BindingDB / ChEBI / ChEMBL / ChemicalBook / DrugBank / Nikkaji / PubChem / PubChem_TPharma / ZINC / Wikipedia search / Google search

Details

SMILES

• ACDLabs 12.01: COC1(C)CC(OC(C1O)C)OC3C(C)C(=O)OC(CC)C(C)(O)C2C(C)C(NC(O2)COCCOC)C(CC(C(C3C)OC4C(C(CC(O4)C)N(C)C)O)(C)O)C
• CACTVS 3.385: CC[CH]1OC(=O)[CH](C)[CH](O[CH]2C[C](C)(OC)[CH](O)[CH](C)O2)[CH](C)[CH](O[CH]3O[CH](C)C[CH]([CH]3O)N(C)C)[C](C)(O)C[CH](C)[CH]4N[CH](COCCOC)O[CH]([CH]4C)[C]1(C)O
• OpenEye OEToolkits 2.0.7: CCC1C(C2C(C(C(CC(C(C(C(C(C(=O)O1)C)OC3CC(C(C(O3)C)O)(C)OC)C)OC4C(C(CC(O4)C)N(C)C)O)(C)O)C)NC(O2)COCCOC)C)(C)O

SMILES CANONICAL

• CACTVS 3.385: CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@H]2C[C@@](C)(OC)[C@@H](O)[C@H](C)O2)[C@H](C)[C@@H](O[C@@H]3O[C@H](C)C[C@@H]([C@H]3O)N(C)C)[C@](C)(O)C[C@@H](C)[C@@H]4N[C@@H](COCCOC)O[C@H]([C@H]4C)[C@]1(C)O
• OpenEye OEToolkits 2.0.7: CC[C@@H]1[C@@]([C@H]2[C@H]([C@H]([C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]3C[C@@]([C@H]([C@@H](O3)C)O)(C)OC)C)O[C@H]4[C@@H]([C@H](C[C@H](O4)C)N(C)C)O)(C)O)C)N[C@H](O2)COCCOC)C)(C)O

InChI

• InChI 1.03: InChI=1S/C42H78N2O14/c1-15-29-42(10,49)37-24(4)32(43-30(56-37)21-52-17-16-50-13)22(2)19-40(8,48)36(58-39-33(45)28(44(11)12)18-23(3)53-39)25(5)34(26(6)38(47)55-29)57-31-20-41(9,51-14)35(46)27(7)54-31/h22-37,39,43,45-46,48-49H,15-21H2,1-14H3/t22-,23-,24+,25+,26-,27+,28+,29-,30-,31+,32+,33-,34+,35+,36-,37-,39+,40-,41-,42-/m1/s1

InChIKey

• InChI 1.03: WLOHNSSYAXHWNR-DWIOZXRMSA-N

SYSTEMATIC NAME

• ACDLabs 12.01: (1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,15R,17S)-3-ethyl-2,10-dihydroxy-15-[(2-methoxyethoxy)methyl]-2,6,8,10,12,17-hexamethyl-5-oxo-9-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-7-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside
• OpenEye OEToolkits 2.0.7: (1~{R},2~{R},3~{R},6~{R},7~{S},8~{S},9~{R},10~{R},12~{R},13~{S},15~{R},17~{S})-9-[(2~{S},3~{R},4~{S},6~{R})-4-(dimethylamino)-6-methyl-3-oxidanyl-oxan-2-yl]oxy-3-ethyl-7-[(2~{R},4~{R},5~{S},6~{S})-4-methoxy-4,6-dimethyl-5-oxidanyl-oxan-2-yl]oxy-15-(2-methoxyethoxymethyl)-2,6,8,10,12,17-hexamethyl-2,10-bis(oxidanyl)-4,16-dioxa-14-azabicyclo[11.3.1]heptadecan-5-one

PDB entries

Showing all 4 items

PDB-6of1:
Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution

PDB-6xz7:
E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).

PDB-6xza:
E. coli 70S ribosome in complex with dirithromycin, and deacylated tRNA(iMet) (focused classification).

PDB-6xzb:
E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification).