GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

paldimycin   Click here for help

GtoPdb Ligand ID: 10843

Synonyms: Antibiotic 273 A | U-70,138 | U-70138F
Compound class: Synthetic organic
Comment: Paldimycin is a mixture of Paldimycins A (CAS 94555-00-7; CID 139597408) and B (CAS 94555-01-8; CID 139597428) which are also known as U-67963 and U-67964 which were derived from paulomycins A and B. It acts as a protein synthesis inhibitor. Paldimycin exhibited good antibacterial activity against Gram-positiive pathogens [2-3].
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 54
Hydrogen bond donors 22
Rotatable bonds 61
Topological polar surface area 1004.96
Molecular weight 2210.61
XLogP -2.67
No. Lipinski's rules broken 3

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@@H](C(=O)O[C@H](C1(O)C(OC)CC(OC1C)OC1C(OC(=O)C(C(SC[C@@H](C(=O)O)NC(=O)C)C)NC(=S)SC[C@@H](C(=O)O)NC(=O)C)C(COC(=O)C)OC(C1O)[C@@]1(O)CC(=O)C(=N)C(=C1O)C(=O)O)C)C.COC1CC(OC2C(OC(=O)C(C(SC[C@@H](C(=O)O)NC(=O)C)C)NC(=S)SC[C@@H](C(=O)O)NC(=O)C)C(COC(=O)C)OC(C2O)[C@@]2(O)CC(=O)C(=N)C(=C2O)C(=O)O)OC(C1(O)[C@@H](OC(=O)C(C)C)C)C
Isomeric SMILES CC[C@@H](C(=O)O[C@H](C1(O)C(OC)CC(OC1C)OC1C(OC(=O)C(C(SC[C@@H](C(=O)O)NC(=O)C)C)NC(=S)SC[C@@H](C(=O)O)NC(=O)C)C(COC(=O)C)OC(C1O)[C@@]1(O)CC(=O)C(=N)C(=C1O)C(=O)O)C)C.COC1CC(OC2C(OC(=O)C(C(SC[C@@H](C(=O)O)NC(=O)C)C)NC(=S)SC[C@@H](C(=O)O)NC(=O)C)C(COC(=O)C)OC(C2O)[C@@]2(O)CC(=O)C(=N)C(=C2O)C(=O)O)OC(C1(O)[C@@H](OC(=O)C(C)C)C)C
InChI InChI=1S/C44H64N4O23S3.C43H62N4O23S3/c1-10-16(2)40(61)68-19(5)44(64)18(4)67-28(11-27(44)65-9)70-34-32(53)36(43(63)12-25(52)30(45)29(35(43)54)39(59)60)69-26(13-66-22(8)51)33(34)71-41(62)31(17(3)73-14-23(37(55)56)46-20(6)49)48-42(72)74-15-24(38(57)58)47-21(7)50;1-15(2)39(60)67-18(5)43(63)17(4)66-27(10-26(43)64-9)69-33-31(52)35(42(62)11-24(51)29(44)28(34(42)53)38(58)59)68-25(12-65-21(8)50)32(33)70-40(61)30(16(3)72-13-22(36(54)55)45-19(6)48)47-41(71)73-14-23(37(56)57)46-20(7)49/h16-19,23-24,26-28,31-34,36,45,53-54,63-64H,10-15H2,1-9H3,(H,46,49)(H,47,50)(H,48,72)(H,55,56)(H,57,58)(H,59,60);15-18,22-23,25-27,30-33,35,44,52-53,62-63H,10-14H2,1-9H3,(H,45,48)(H,46,49)(H,47,71)(H,54,55)(H,56,57)(H,58,59)/t16-,17?,18?,19-,23-,24-,26?,27?,28?,31?,32?,33?,34?,36?,43+,44?;16?,17?,18-,22-,23-,25?,26?,27?,30?,31?,32?,33?,35?,42+,43?/m00/s1
InChI Key VSHJMNNDPYEUOT-ILYCIZJESA-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/)