Secondary metabolite: Gymnopeptide B



Gymnopeptide B
Summary
Molecular formula: C85H152N18O19
SMILES: O=C1CN(C)C(=O)[C@@H](NC(=O)[C@H](C)N(C)C(=O)[C@H](C(C)C)N(C)C(=O)CN(C)C(=O)[C@@H](NC(=O)[C@H](C(C)C)N(C)C(=O)[C@H](C)NC(=O)[C@H](C(C)C)N(C)C(=O)[C@@H](NC(=O)[C@@H](N(C(=O)[C@@H](NC(=O)[C@@H](N(C(=O)[C@@H](NC(=O)[C@@H](N(C(=O)[C@@H](NC(=O)[C@@H](N(C(=O)[C@@H](N1)C)C)C(C)C)C)C)C(C)C)[C@H](O)C)C)C(C)C)C(C)C)C)C(C)C)C(C)C)C(C)C)C(C)C
InChI: InChI=1S/C85H152N18O19/c1-40(2)58-80(117)94(28)38-56(105)86-51(23)77(114)98(32)63(44(9)10)71(108)87-52(24)79(116)100(34)66(47(15)16)76(113)93-62(55(27)104)84(121)103(37)68(49(19)20)75(112)92-61(43(7)8)83(120)102(36)67(48(17)18)74(111)91-60(42(5)6)82(119)101(35)64(45(11)12)72(109)88-53(25)78(115)99(33)65(46(13)14)73(110)90-59(41(3)4)81(118)95(29)39-57(106)97(31)69(50(21)22)85(122)96(30)54(26)70(107)89-58/h40-55,58-69,104H,38-39H2,1-37H3,(H,86,105)(H,87,108)(H,88,109)(H,89,107)(H,90,110)(H,91,111)(H,92,112)(H,93,113)/t51-,52-,53-,54-,55+,58-,59-,60-,61-,62-,63-,64-,65-,66-,67-,68-,69-/m0/s1
InChIKey: HMASTEQXASMBFL-OWVWYMDTSA-N
Chemical classification
Kingdom: Organic compounds
Super class: Organic acids and derivatives
Class: Carboxylic acids and derivatives
Sub class: Amino acids, peptides, and analogues
Synonymous chemical names:
gymnopeptide b
Chemical structure download



Gymnopeptide B
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 1730.26
Log P RDKit 0.09
Topological polar surface area (Å2) RDKit 456.13
Number of hydrogen bond acceptors RDKit 19
Number of hydrogen bond donors RDKit 9
Number of carbon atoms RDKit 85
Number of heavy atoms RDKit 122
Number of heteroatoms RDKit 37
Number of nitrogen atoms RDKit 18
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 17
Stereochemical complexity RDKit 0.2
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 18
Number of sp3 hybridized carbon atoms RDKit 67
Fraction of sp3 hybridized carbon atoms (Fsp3) RDKit 0.79
Shape complexity RDKit 0.79
Number of rotatable bonds SwissADME 12
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 1
Number of aliphatic rings RDKit 1
Number of aromatic carbocycles RDKit 0
Number of aromatic heterocycles RDKit 0
Number of aromatic rings RDKit 0
Total number of rings RDKit 1
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 1
Number of saturated rings RDKit 1
Number of Smallest Set of Smallest Rings (SSSR) RDKit 1



Gymnopeptide B
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 3
Lipinski’s rule of 5 filter RDKit Failed
Number of Ghose filter violations RDKit 3
Ghose filter RDKit Failed
Veber filter RDKit Bad
Egan filter RDKit Bad
Pfizer’s 3/75 filter RDKit Good
GSK 4/400 filter RDKit Bad
Number of Leadlikeness violations SwissADME 3
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.12



Gymnopeptide B
ADMET properties
Property nameToolProperty value
Bioavailability score SwissADME 0.17
Solubility class [ESOL] SwissADME Insoluble
Solubility class [Silicos-IT] SwissADME Poorly soluble
Blood Brain Barrier permeation SwissADME No
Gastrointestinal absorption SwissADME Low
Log Kp (Skin permeation, cm/s) SwissADME -11.88
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME Yes




Designed by R.P. Vivek-Ananth, M Karthikeyan and Ajaya Kumar Sahoo