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muraymycin D2   Click here for help

GtoPdb Ligand ID: 13501

Synonyms: muramycin D2
PDB Ligand
Compound class: Natural product
Comment: Muraymycin D2 is a nucleoside antibacterial compound, initially isolated from the culture filtrate of Streptomyces sp. LL-AA896 [1]. It inhibits Phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY).
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 27
Hydrogen bond donors 15
Rotatable bonds 26
Topological polar surface area 420.41
Molecular weight 915.95
XLogP -6.38
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 CC(C)C[C@@H](C(=O)NCCCN[C@@H]([C@@H]([C@@H]1[C@H]([C@H]([C@H](N2C=CC(=O)NC2=O)O1)O)O)O[C@H]3[C@@H]([C@@H]([C@@H](CN)O3)O)O)C(=O)O)NC(=O)[C@H]([C@@H]4CCNC(=N4)N)NC(=O)N[C@@H](C(C)C)C(=O)O
Isomeric SMILES CC(C)C[C@@H](C(=O)NCCCN[C@@H]([C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O)O[C@H]3[C@@H]([C@@H]([C@H](O3)CN)O)O)C(=O)O)NC(=O)[C@H]([C@@H]4CCNC(=N4)N)NC(=O)N[C@@H](C(C)C)C(=O)O
InChI InChI=1S/C37H61N11O16/c1-14(2)12-17(43-30(55)21(16-6-10-42-35(39)44-16)47-36(60)46-20(15(3)4)32(56)57)29(54)41-9-5-8-40-22(33(58)59)27(64-34-26(53)23(50)18(13-38)62-34)28-24(51)25(52)31(63-28)48-11-7-19(49)45-37(48)61/h7,11,14-18,20-28,31,34,40,50-53H,5-6,8-10,12-13,38H2,1-4H3,(H,41,54)(H,43,55)(H,56,57)(H,58,59)(H3,39,42,44)(H,45,49,61)(H2,46,47,60)/t16-,17-,18+,20-,21-,22-,23+,24-,25+,26+,27-,28-,31+,34-/m0/s1
InChI Key RRTIONDZEJYWBN-VDXVSALRSA-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
(2S)-2-[[(1S)-2-[[(2S)-1-[3-[[(1S,2S)-2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy-1-carboxy-2-[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]ethyl]amino]propylamino]-4-methyl-1-oxopentan-2-yl]amino]-1-[(6S)-2-amino-1,4,5,6-tetrahydropyrimidin-6-yl]-2-oxoethyl]carbamoylamino]-3-methylbutanoic acid
Synonyms Click here for help
muramycin D2
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Muraymycin
Other databases
BindingDB Ligand 50343928
CAS Registry No. 474328-38-6 (source: Scifinder)
ChEBI CHEBI:178053
ChEMBL Ligand CHEMBL1780216
GtoPdb PubChem SID 500839911
PubChem CID 45142130
RCSB PDB Ligand 57M
Search Google for chemical match using the InChIKey RRTIONDZEJYWBN-VDXVSALRSA-N
Search Google for chemicals with the same backbone RRTIONDZEJYWBN
UniChem Compound Search for chemical match using the InChIKey RRTIONDZEJYWBN-VDXVSALRSA-N
UniChem Connectivity Search for chemical match using the InChIKey RRTIONDZEJYWBN-VDXVSALRSA-N