Natural Product: NPC477325

Natural Product IDNPC477325
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
[(2S,3R,4R,5S,6S)-5-[(2S,3R,4S,5R,6S)-3,4-dihydroxy-6-methyl-5-octanoyloxyoxan-2-yl]oxy-6-methyl-2-[[(1S,3R,4S,5R,6R,8R,10S,22S,23S,24S,26R)-4,5,26-trihydroxy-6,24-dimethyl-20-oxo-10-pentyl-2,7,9,21,25-pentaoxatricyclo[20.3.1.03,8]hexacosan-23-yl]oxy]-4-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-3-yl] decanoate
IUPAC Name [(2S,3R,4R,5S,6S)-5-[(2S,3R,4S,5R,6S)-3,4-dihydroxy-6-methyl-5-octanoyloxyoxan-2-yl]oxy-6-methyl-2-[[(1S,3R,4S,5R,6R,8R,10S,22S,23S,24S,26R)-4,5,26-trihydroxy-6,24-dimethyl-20-oxo-10-pentyl-2,7,9,21,25-pentaoxatricyclo[20.3.1.03,8]hexacosan-23-yl]oxy]-4-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-3-yl] decanoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 118716655
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey JEMWDSYXQWEUBC-OVRXSPRISA-N
Standard InCHI InChI=1S/C64H112O24/c1-9-12-15-17-19-24-30-35-44(67)84-59-58(88-60-50(73)47(70)45(68)36(4)76-60)55(85-61-51(74)49(72)53(38(6)78-61)82-42(65)33-28-22-16-13-10-2)40(8)80-64(59)86-54-39(7)79-62-52(75)56(54)83-43(66)34-29-25-21-18-20-23-27-32-41(31-26-14-11-3)81-63-57(87-62)48(71)46(69)37(5)77-63/h36-41,45-64,68-75H,9-35H2,1-8H3/t36-,37+,38-,39-,40-,41-,45-,46-,47+,48-,49-,50+,51+,52+,53-,54-,55-,56-,57+,58+,59+,60-,61-,62-,63-,64-/m0/s1
SMILES CCCCCCCCCC(=O)O[C@@H]1[C@@H]([C@H]([C@@H](O[C@H]1O[C@H]2[C@@H](O[C@@H]3[C@@H]([C@@H]2OC(=O)CCCCCCCCC[C@@H](O[C@H]4[C@H](O3)[C@H]([C@H]([C@H](O4)C)O)O)CCCCC)O)C)C)O[C@H]5[C@@H]([C@@H]([C@H]([C@@H](O5)C)OC(=O)CCCCCCC)O)O)O[C@H]6[C@@H]([C@@H]([C@H]([C@@H](O6)C)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1264.75 Volume:   1267.217
?
Van der Waals volume.
Dense:   0.998 LogP:   5.589
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.852
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.447
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The logarithm of aqueous solubility value.
Rotatable Bonds:   28.0 Rigid Bonds:   49.0
TPSA:   333.04
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   8.0 Rings:   6.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.029 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.91 Fsp3:   0.953
MCE-18:   120.32
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.999 Fluc inhibitor:   0.333
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.54 Promiscuous compounds:   0.035

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.558 MDCK Permeability:   -5.037
Pgp-inhibitor:   0.0 Pgp-substrate:   0.995
PAMPA:   0.998
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
Human Intestinal Absorption (HIA):   0.463
20% Bioavailability (F20%):   0.25 30% Bioavailability (F30%):   0.82
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.999
Plasma Protein Binding (PPB):   95.742% Volume Distribution (VD):   0.133
Fu: 3.707%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.825
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.36

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.251
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.65
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.982
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  0.955 Half-life (T1/2):  3.208

ADMET: Toxicity

hERG Blockers:  0.066 hERG Blockers (10um):  0.362
Human Hepatotoxicity (H-HT):  0.348 Drug-induced Liver Injury (DILI):  0.985
AMES Toxicity:  0.506 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.005 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.616 Drug-induced Nephrotoxicity:  0.959
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.724
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.407
BCF:   1.039
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
IGC50:   4.888
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.137
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.945
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota Whole Plant Dongshan, Nanjing, Jiangsu Province, China 2012-NOV PMID[25314138]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[38192648]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
UNPD: Universal Natural Products Database [PMID: 23638153].
StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
MetaboLights: a metabolomics database [PMID: 27010336].
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT659 Cell line SMMC-7721 Homo sapiens IC50 > 10000 nM PMID[25314138]
NPT65 Cell line HepG2 Homo sapiens IC50 = 4900 nM PMID[25314138]
NPT1045 Cell line U2OS Homo sapiens IC50 > 10000 nM PMID[25314138]
NPT83 Cell line MCF7 Homo sapiens IC50 = 9800 nM PMID[25314138]
NPT2 Others Unspecified n.a. IC50 = 6000 nM PMID[25314138]
NPT2 Others Unspecified n.a. IC50 > 10000 nM PMID[25314138]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC477325 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC113745
1.0 High Similarity NPC477320
1.0 High Similarity NPC477323
1.0 High Similarity NPC609436
0.9412 High Similarity NPC146380
0.9315 High Similarity NPC267592
0.9067 High Similarity NPC307400
0.9067 High Similarity NPC27289
0.9041 High Similarity NPC477326
0.8933 High Similarity NPC477319
0.8816 High Similarity NPC143421
0.8767 High Similarity NPC604005
0.8767 High Similarity NPC605014
0.8608 High Similarity NPC123204
0.859 High Similarity NPC290012
0.8356 Intermediate Similarity NPC281563
0.825 Intermediate Similarity NPC183888
0.825 Intermediate Similarity NPC259294
0.8025 Intermediate Similarity NPC126685
0.7917 Intermediate Similarity NPC606819
0.7875 Intermediate Similarity NPC472204
0.7821 Intermediate Similarity NPC600446
0.7821 Intermediate Similarity NPC605013
0.7561 Intermediate Similarity NPC483170
0.75 Intermediate Similarity NPC109887
0.7237 Intermediate Similarity NPC477350
0.7229 Intermediate Similarity NPC119583
0.7059 Intermediate Similarity NPC115013
0.7033 Intermediate Similarity NPC124878
0.7033 Intermediate Similarity NPC231888
0.6957 Remote Similarity NPC35338
0.6957 Remote Similarity NPC204214
0.6957 Remote Similarity NPC92283
0.686 Remote Similarity NPC169345
0.6842 Remote Similarity NPC10121
0.6842 Remote Similarity NPC198918
0.6829 Remote Similarity NPC89843
0.6774 Remote Similarity NPC63404
0.6747 Remote Similarity NPC477344
0.6667 Remote Similarity NPC477317
0.6667 Remote Similarity NPC477318
0.6627 Remote Similarity NPC478734
0.6591 Remote Similarity NPC184915
0.6591 Remote Similarity NPC224953
0.6585 Remote Similarity NPC22742
0.6585 Remote Similarity NPC477349
0.6585 Remote Similarity NPC477346
0.6512 Remote Similarity NPC472205
0.6471 Remote Similarity NPC478733
0.6444 Remote Similarity NPC44782
0.6395 Remote Similarity NPC146992
0.6395 Remote Similarity NPC85759
0.6322 Remote Similarity NPC297768
0.6292 Remote Similarity NPC478731
0.625 Remote Similarity NPC294748
0.625 Remote Similarity NPC478730
0.618 Remote Similarity NPC238264
0.618 Remote Similarity NPC476087
0.618 Remote Similarity NPC475667
0.618 Remote Similarity NPC477345
0.6162 Remote Similarity NPC10883
0.6154 Remote Similarity NPC163409
0.6145 Remote Similarity NPC477329
0.6136 Remote Similarity NPC173328
0.6125 Remote Similarity NPC478729
0.6111 Remote Similarity NPC238056
0.6111 Remote Similarity NPC478732
0.6067 Remote Similarity NPC186992
0.6044 Remote Similarity NPC475270
0.6044 Remote Similarity NPC475327
0.6024 Remote Similarity NPC477330
0.602 Remote Similarity NPC77651
0.5978 Remote Similarity NPC475525
0.5978 Remote Similarity NPC475540
0.5977 Remote Similarity NPC158302
0.5914 Remote Similarity NPC476066
0.5859 Remote Similarity NPC28069
0.5851 Remote Similarity NPC475164
0.5843 Remote Similarity NPC479061
0.5833 Remote Similarity NPC477328
0.5806 Remote Similarity NPC472200
0.5795 Remote Similarity NPC479059
0.5789 Remote Similarity NPC473605
0.5789 Remote Similarity NPC475375
0.5778 Remote Similarity NPC479060
0.5766 Remote Similarity NPC147032
0.5728 Remote Similarity NPC471025
0.567 Remote Similarity NPC475241
0.566 Remote Similarity NPC472352
0.5604 Remote Similarity NPC479058
0.5591 Remote Similarity NPC162925
0.5579 Remote Similarity NPC269318
0.5529 Remote Similarity NPC475425
0.5506 Remote Similarity NPC477331
0.5506 Remote Similarity NPC477332
0.5495 Remote Similarity NPC60849
0.5435 Remote Similarity NPC44682
0.5422 Remote Similarity NPC169085
0.5413 Remote Similarity NPC471024
0.5385 Remote Similarity NPC290276
0.5361 Remote Similarity NPC478728
0.5306 Remote Similarity NPC478727
0.5269 Remote Similarity NPC478724
0.5244 Remote Similarity NPC9763
0.5161 Remote Similarity NPC478722
0.5161 Remote Similarity NPC478725
0.5106 Remote Similarity NPC478723
0.5094 Remote Similarity NPC611287
0.5093 Remote Similarity NPC600721
0.5093 Remote Similarity NPC605872
0.5091 Remote Similarity NPC471026
0.5047 Remote Similarity NPC600672

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC477325 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
A: chemistry similarity;
B: biological targets similarity;
C: networks similarity;
D: cell-based bioactivity similarity;
E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data