omadacycline   Click here for help

GtoPdb Ligand ID: 10839

Synonyms: amadacycline | compound 6 [PMID: 21302930] | Nuzyra® | PTK-0796 | PTK0796
Approved drug PDB Ligand
omadacycline is an approved drug (FDA (2018))
Compound class: Synthetic organic
Comment: Omadacycline (PTK-0796) is an oral, tetracycline-like antibacterial [1].
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 10
Hydrogen bond donors 6
Rotatable bonds 7
Topological polar surface area 176.66
Molecular weight 556.29
XLogP 2.54
No. Lipinski's rules broken 1
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES CN([C@@H]1C(=O)C(=C([C@@]2([C@H]1C[C@@H]1Cc3c(cc(c(c3C(=C1C2=O)O)O)CNCC(C)(C)C)N(C)C)O)O)C(=O)N)C
Isomeric SMILES CN([C@@H]1C(=O)C(=C([C@@]2([C@H]1C[C@@H]1Cc3c(cc(c(c3C(=C1C2=O)O)O)CNCC(C)(C)C)N(C)C)O)O)C(=O)N)C
InChI InChI=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
InChI Key VJYKVCURWJGLPG-IQZGDKDPSA-N
Classification Click here for help
Compound class Synthetic organic
Approved drug? Yes (FDA (2018))
IUPAC Name Click here for help
(4S,4aS,5aR,12aR)-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12a-tetrahydroxy-3,12-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide
International Nonproprietary Names Click here for help
INN number INN
9186 omadacycline
Synonyms Click here for help
amadacycline | compound 6 [PMID: 21302930] | Nuzyra® | PTK-0796 | PTK0796
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Omadacycline (PTK-0796)
Other databases
CAS Registry No. 389139-89-3 (source: WHO INN record)
ChEMBL Ligand CHEMBL1689772
GtoPdb PubChem SID 405560280
PubChem CID 54697325
RCSB PDB Ligand U3B
Search Google for chemical match using the InChIKey VJYKVCURWJGLPG-IQZGDKDPSA-N
Search Google for chemicals with the same backbone VJYKVCURWJGLPG
Search PubMed clinical trials omadacycline
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UniChem Compound Search for chemical match using the InChIKey VJYKVCURWJGLPG-IQZGDKDPSA-N
UniChem Connectivity Search for chemical match using the InChIKey VJYKVCURWJGLPG-IQZGDKDPSA-N