pacidamycin   Click here for help

GtoPdb Ligand ID: 13473

Compound class: Natural product
Comment: Pacidamycin is a nucleoside antibacterial compound that was obtained from the culture broth of Streptomyces coeruleorubidus [2-3]. It inhibits phospho-N-acetylmuramoyl-pentapeptide-transferase (MraY, translocase I), an essential enzyme in bacterial peptidoglycan biosynthesis.
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 20
Hydrogen bond donors 10
Rotatable bonds 21
Topological polar surface area 294.09
Molecular weight 805.83
XLogP -4.94
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 C[C@@H](C(=O)N[C@@H]([C@H](C)N(C)C(=O)[C@H](CC1=CC=C(C=C1)O)N)C(=O)NC[C@H]2C[C@H]([C@H](N3C=CC(=O)NC3=O)O2)O)NC(=O)N[C@@H](CC4=CNC5=C4C=CC=C5)C(=O)O
Isomeric SMILES C[C@@H]([C@@H](C(=O)NC[C@H]1C[C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)NC(=O)[C@H](C)NC(=O)N[C@@H](CC3=CNC4=CC=CC=C43)C(=O)O)N(C)C(=O)[C@H](CC5=CC=C(C=C5)O)N
InChI InChI=1S/C38H47N9O11/c1-19(42-37(56)43-28(36(54)55)15-22-17-40-27-7-5-4-6-25(22)27)32(51)45-31(20(2)46(3)34(53)26(39)14-21-8-10-23(48)11-9-21)33(52)41-18-24-16-29(49)35(58-24)47-13-12-30(50)44-38(47)57/h4-13,17,19-20,24,26,28-29,31,35,40,48-49H,14-16,18,39H2,1-3H3,(H,41,52)(H,45,51)(H,54,55)(H2,42,43,56)(H,44,50,57)/t19-,20-,24+,26-,28-,29+,31-,35+/m0/s1
InChI Key HKPRQZOLLXYDJX-KOGPLRHPSA-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. Chen RH, Buko AM, Whittern DN, McAlpine JB. (1989)
Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. II. Isolation and structural elucidation.
J Antibiot (Tokyo), 42 (4): 512-20. [PMID:2498264]
3. Fernandes PB, Swanson RN, Hardy DJ, Hanson CW, Coen L, Rasmussen RR, Chen RH. (1989)
Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. III. Microbiologic profile.
J Antibiot (Tokyo), 42 (4): 521-6. [PMID:2498265]
4. 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]
5. 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]