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xenorceptide A2   Click here for help

GtoPdb Ligand ID: 14124

Compound class: Natural product
Comment: Xenorceptide A2 is a natural product from Xenorhabdus nematophila that targets BamA (bioRxiv preprint [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 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 40
Hydrogen bond donors 23
Rotatable bonds 34
Topological polar surface area 646.35
Molecular weight 1641.75
XLogP -4.41
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)C1C(=O)NC([C@@H](C2=CC3=C(C=C2)C(=CN3)CC(C(=O)N1)N)C(=O)N)C(=O)NC(C)C(=O)NC4CC5=CC=C(C=C5)C(C(C(=O)NC6CC7=CNC8=C7C=CC(=C8)[C@@H](CCNC(=N)N)C(C(=O)NC(C)C(=O)NC(CC9=CC=CC=C9)C(=O)NC(CC%10=CNC=N%10)C(=O)O)NC(=O)C(CCC(=O)O)NC6=O)NC(=O)CNC4=O)C(=O)N
Isomeric SMILES CCC(C)C1C(=O)NC([C@@H](C2=CC3=C(C=C2)C(=CN3)CC(C(=O)N1)N)C(=O)N)C(=O)NC(C)C(=O)NC4CC5=CC=C(C=C5)C(C(NC(=O)CNC4=O)C(=O)NC6CC7=CNC8=C7C=CC(=C8)[C@H](C(NC(=O)C(NC6=O)CCC(=O)O)C(=O)NC(C)C(=O)NC(CC9=CC=CC=C9)C(=O)NC(CC%10=CNC=N%10)C(=O)O)CCNC(=N)N)C(=O)N
InChI InChI=1S/C79H96N22O18/c1-5-35(2)61-74(114)101-64(60(66(82)106)42-16-18-46-43(30-87-52(46)27-42)25-49(80)69(109)99-61)76(116)92-37(4)67(107)94-53-24-39-11-13-40(14-12-39)59(65(81)105)63(98-57(102)33-89-70(53)110)77(117)96-55-28-44-31-88-51-26-41(15-17-47(44)51)48(21-22-86-79(83)84)62(100-71(111)50(93-73(55)113)19-20-58(103)104)75(115)91-36(3)68(108)95-54(23-38-9-7-6-8-10-38)72(112)97-56(78(118)119)29-45-32-85-34-90-45/h6-18,26-27,30-32,34-37,48-50,53-56,59-64,87-88H,5,19-25,28-29,33,80H2,1-4H3,(H2,81,105)(H2,82,106)(H,85,90)(H,89,110)(H,91,115)(H,92,116)(H,93,113)(H,94,107)(H,95,108)(H,96,117)(H,97,112)(H,98,102)(H,99,109)(H,100,111)(H,101,114)(H,103,104)(H,118,119)(H4,83,84,86)/t35?,36?,37?,48-,49?,50?,53?,54?,55?,56?,59?,60-,61?,62?,63?,64?/m1/s1
InChI Key DQSGFVGNYMGMKW-KKYXUIGUSA-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. Modaresi SM, Sugiyama R, Tram NDT, Jakob RP, Phan C, Saei AA, Morishita Y, Mühlethaler T, Lim J, Ritz D. (2024)
Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA.
bioRxiv, preprint. DOI: 10.1101/2024.12.16.628070