caprazamycin B   Click here for help

GtoPdb Ligand ID: 13474

Compound class: Natural product
Comment: Caprazamycin B is a liponucleoside antibacterial compound, with activity against Gram-positive bacteria and mycobacteria, that was obtained from the culture broth of the actinomycete strain Streptomyces sp. MK730-62F2 [3-4]. It inhibits phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY, translocase I) [5], an essential enzyme in bacterial peptidoglycan biosynthesis.
2D Structure
Click here for help

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.

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

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.

✖
Hydrogen bond acceptors 27
Hydrogen bond donors 7
Rotatable bonds 33
Topological polar surface area 360.71
Molecular weight 1146.28
XLogP 0.21
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

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/)

✖
Canonical SMILES CC(C)CCCCCCCCCCC(CC(=O)OC1CN(C)C(C(C2C(C(C(N3C=CC(=O)NC3=O)O2)O)O)OC4C(C(C(CN)O4)O)O)C(=O)N(C)C1C(=O)O)OC(=O)CC(C)CC(=O)OC5C(C(C(C(C)O5)OC)OC)OC
Isomeric SMILES CC1C(C(C(C(O1)OC(=O)CC(C)CC(=O)OC(CCCCCCCCCCC(C)C)CC(=O)OC2CN(C(C(=O)N(C2C(=O)O)C)C(C3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)OC5C(C(C(O5)CN)O)O)C)OC)OC)OC
InChI InChI=1S/C53H87N5O22/c1-27(2)18-16-14-12-10-11-13-15-17-19-30(75-34(60)22-28(3)23-35(61)78-52-47(73-9)46(72-8)43(71-7)29(4)74-52)24-36(62)76-32-26-56(5)38(48(67)57(6)37(32)50(68)69)44(80-51-42(66)39(63)31(25-54)77-51)45-40(64)41(65)49(79-45)58-21-20-33(59)55-53(58)70/h20-21,27-32,37-47,49,51-52,63-66H,10-19,22-26,54H2,1-9H3,(H,68,69)(H,55,59,70)
InChI Key IDKBSYZJTHLMLI-UHFFFAOYSA-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. ANDERSON JS, MATSUHASHI M, HASKIN MA, STROMINGER JL. (1965)
LIPID-PHOSPHOACETYLMURAMYL-PENTAPEPTIDE AND LIPID-PHOSPHODISACCHARIDE-PENTAPEPTIDE: PRESUMED MEMBRANE TRANSPORT INTERMEDIATES IN CELL WALL SYNTHESIS.
Proc Natl Acad Sci U S A, 53 (4): 881-9. [PMID:14324547]
2. Heydanek Jr MG, Neuhaus FC. (1969)
The initial stage in peptidoglycan synthesis. IV. Solubilization of phospho-N-acetylmuramyl-pentapeptide translocase.
Biochemistry, 8 (4): 1474-81. [PMID:5805290]
3. Igarashi M, Nakagawa N, Doi N, Hattori S, Naganawa H, Hamada M. (2003)
Caprazamycin B, a novel anti-tuberculosis antibiotic, from Streptomyces sp.
J Antibiot (Tokyo), 56 (6): 580-3. [PMID:12931868]
4. Igarashi M, Takahashi Y, Shitara T, Nakamura H, Naganawa H, Miyake T, Akamatsu Y. (2005)
Caprazamycins, novel lipo-nucleoside antibiotics, from Streptomyces sp. II. Structure elucidation of caprazamycins.
J Antibiot (Tokyo), 58 (5): 327-37. [PMID:16060385]
5. Ishizaki Y, Hayashi C, Inoue K, Igarashi M, Takahashi Y, Pujari V, Crick DC, Brennan PJ, Nomoto A. (2013)
Inhibition of the first step in synthesis of the mycobacterial cell wall core, catalyzed by the GlcNAc-1-phosphate transferase WecA, by the novel caprazamycin derivative CPZEN-45.
J Biol Chem, 288 (42): 30309-30319. [PMID:23986448]
6. STRUVE WG, NEUHAUS FC. (1965)
EVIDENCE FOR AN INITIAL ACCEPTOR OF UDP-NAC-MURAMYL-PENTAPEPTIDE IN THE SYNTHESIS OF BACTERIAL MUCOPEPTIDE.
Biochem Biophys Res Commun, 18: 6-12. [PMID:14265759]