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- ChemComp-U3B: Omadacycline -

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Basic information

EntryDatabase: PDB chemical components / ID: U3B
NameName: Omadacycline
Synonyms: Omadacycline; (4S,4aS,5aR,12aR)-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12a-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide

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Chemical information

Composition
Formula: C29H40N4O7 / Number of atoms: 80 / Formula weight: 556.65 / Formal charge: 0
Others

8ca7

Type: non-polymer / PDB classification: HETAIN / Three letter code: U3B / Ideal coordinates details: Corina / Model coordinates PDB-ID: 8CA7
History
Create componentJan 24, 2023
Modify nameJan 26, 2023
Modify aromatic flagJul 25, 2023
Initial releaseAug 2, 2023
External linksUniChem / ChemSpider / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

CACTVS 3.385CN(C)[CH]1[CH]2C[CH]3Cc4c(cc(CNCC(C)(C)C)c(O)c4C(=C3C(=O)[C]2(O)C(=C(C(N)=O)C1=O)O)O)N(C)C
OpenEye OEToolkits 2.0.7CC(C)(C)CNCc1cc(c2c(c1O)C(=C3C(C2)CC4C(C(=O)C(=C(C4(C3=O)O)O)C(=O)N)N(C)C)O)N(C)C

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SMILES CANONICAL

CACTVS 3.385CN(C)[C@H]1[C@@H]2C[C@@H]3Cc4c(cc(CNCC(C)(C)C)c(O)c4C(=C3C(=O)[C@]2(O)C(=C(C(N)=O)C1=O)O)O)N(C)C
OpenEye OEToolkits 2.0.7CC(C)(C)CNCc1cc(c2c(c1O)C(=C3[C@@H](C2)C[C@H]4[C@@H](C(=O)C(=C([C@]4(C3=O)O)O)C(=O)N)N(C)C)O)N(C)C

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InChI

InChI 1.06InChI=1S/C29H40N4O7/c1-28(2,3)12-31-11-14-10-17(32(4)5)15-8-13-9-16-21(33(6)7)24(36)20(27(30)39)26(38)29(16,40)25(37)18(13)23(35)19(15)22(14)34/h10,13,16,21,31,34-35,38,40H,8-9,11-12H2,1-7H3,(H2,30,39)/t13-,16-,21-,29-/m0/s1

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InChIKey

InChI 1.06VJYKVCURWJGLPG-IQZGDKDPSA-N

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PDB entries

Showing all 1 items

PDB-8ca7:
Omadacycline and spectinomycin bound to the 30S ribosomal subunit head

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