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
Click here for help
Click here for structure editor
Physico-chemical Properties
Click here for help
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
Click here for help
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