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pipacycline   Click here for help

GtoPdb Ligand ID: 13612

Synonyms: mepicycline
Compound class: Synthetic organic
Comment: Pipacycline is a tetracycline antibacterial compound. Note that the structure shown here matches the CAS-assigned structure. The PubChem link, provided in the table below, is to their standardized chemical structure (CID 54686184), although this is not an exact structural match.
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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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 13
Hydrogen bond donors 7
Rotatable bonds 7
Topological polar surface area 194.34
Molecular weight 586.63
XLogP -1.35
No. Lipinski's rules broken 3

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES C[C@]1(C2=CC=CC(=C2C(=O)C3=C([C@]4([C@@]([H])(C[C@@]31[H])[C@@H](C(=C(C4=O)C(=O)NCN5CCN(CC5)CCO)O)N(C)C)O)O)O)O
Isomeric SMILES O[C@@]12[C@@](C[C@]3(C(=C1O)C(=O)C=4C([C@@]3(C)O)=CC=CC4O)[H])([C@H](N(C)C)C(O)=C(C(NCN5CCN(CCO)CC5)=O)C2=O)[H]
InChI InChI=1S/C29H38N4O9/c1-28(41)15-5-4-6-18(35)19(15)23(36)20-16(28)13-17-22(31(2)3)24(37)21(26(39)29(17,42)25(20)38)27(40)30-14-33-9-7-32(8-10-33)11-12-34/h4-6,16-17,22,34-35,37-38,41-42H,7-14H2,1-3H3,(H,30,40)/t16-,17-,22-,28+,29-/m0/s1
InChI Key XATZHCXBMKRRDO-REHNUXHNSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Chopra I, Hawkey PM, Hinton M. (1992)
Tetracyclines, molecular and clinical aspects.
J Antimicrob Chemother, 29 (3): 245-77. [PMID:1592696]
2. Chopra I, Roberts M. (2001)
Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance.
Microbiol Mol Biol Rev, 65 (2): 232-60 ; second page, table of contents. [PMID:11381101]