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amphomycin   Click here for help

GtoPdb Ligand ID: 13516

Synonyms: glumamycin
Compound class: Natural product
Comment: Amphomycin is a lipopeptide antibacterial compound, initially isolated from the culture filtrate of Streptomyces canus [1]. Functionally, the compound inhibits phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY, translocase I), an essential enzyme in bacterial peptidoglycan biosynthesis. Amphomycin is approved as a veterinary drug.
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 33
Hydrogen bond donors 15
Rotatable bonds 48
Topological polar surface area 506.84
Molecular weight 1290.42
XLogP -0.94
No. Lipinski's rules broken 4

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 CCC(C)CCCCC/C=C/CC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H]([C@@H](C)C(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@H]([C@H](C)N)C(=O)N[C@@H](C(C)C)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C)[C@H]2C(=O)N3CCCC[C@@H]3C(=O)N2
Isomeric SMILES CCC(C)CCCCC/C=C/CC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H]([C@@H](C)C(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@H]([C@H](C)N)C(=O)N[C@@H](C(C)C)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C)[C@H]2C(=O)N3CCCC[C@@H]3C(=O)N2
InChI InChI=1S/C58H91N13O20/c1-8-30(4)18-13-11-9-10-12-14-21-39(72)63-36(26-44(79)80)51(83)68-46(31(5)58(90)91)54(86)65-35(25-43(77)78)50(82)60-27-40(73)64-34(24-42(75)76)49(81)61-28-41(74)66-47(32(6)59)55(87)67-45(29(2)3)56(88)71-23-17-20-38(71)52(84)62-33(7)48-57(89)70-22-16-15-19-37(70)53(85)69-48/h12,14,29-38,45-48H,8-11,13,15-28,59H2,1-7H3,(H,60,82)(H,61,81)(H,62,84)(H,63,72)(H,64,73)(H,65,86)(H,66,74)(H,67,87)(H,68,83)(H,69,85)(H,75,76)(H,77,78)(H,79,80)(H,90,91)/b14-12+/t30?,31-,32+,33+,34+,35+,36+,37-,38+,45+,46+,47-,48+/m1/s1
InChI Key XBNDESPXQUOOBQ-LSMLZNGOSA-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/)
Classification Click here for help
Compound class Natural product
IUPAC Name Click here for help
(2R,3S)-4-[[(2S)-1-[[2-[[(2S)-1-[[2-[[(2R,3S)-1-[[(2S)-1-[(2S)-2-[[(1S)-1-[(3S,9aR)-1,4-dioxo-3,6,7,8,9,9a-hexahydro-2H-pyrido[1,2-a]pyrazin-3-yl]ethyl]carbamoyl]pyrrolidin-1-yl]-3-methyl-1-oxobutan-2-yl]amino]-3-amino-1-oxobutan-2-yl]amino]-2-oxoethyl]amino]-3-carboxy-1-oxopropan-2-yl]amino]-2-oxoethyl]amino]-3-carboxy-1-oxopropan-2-yl]amino]-3-[[(2S)-3-carboxy-2-[[(E)-10-methyldodec-3-enoyl]amino]propanoyl]amino]-2-methyl-4-oxobutanoic acid
Synonyms Click here for help
glumamycin
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Amphomycin
Other databases
CAS Registry No. 1402-82-0 (source: Scifinder)
DrugBank Ligand DB11499
DrugCentral Ligand 5550
GtoPdb PubChem SID 500839926
PubChem CID 91663250
Search Google for chemical match using the InChIKey XBNDESPXQUOOBQ-LSMLZNGOSA-N
Search Google for chemicals with the same backbone XBNDESPXQUOOBQ
UniChem Compound Search for chemical match using the InChIKey XBNDESPXQUOOBQ-LSMLZNGOSA-N
UniChem Connectivity Search for chemical match using the InChIKey XBNDESPXQUOOBQ-LSMLZNGOSA-N