Natural Product: NPC478731

Natural Product IDNPC478731
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
JTHTZSOMPITLTF-DSHOZJNWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11286265
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003918] Saccharolipids

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 JTHTZSOMPITLTF-DSHOZJNWSA-N
Standard InCHI InChI=1S/C55H94O24/c1-11-12-18-21-34-22-19-16-14-13-15-17-20-23-36(58)74-48-45(77-52-43(65)42(64)44(32(9)70-52)76-51(67)28(5)30(7)57)33(10)71-55(49(48)75-37(59)24-26(2)3)79-47-41(63)39(61)35(25-68-50(66)27(4)29(6)56)73-54(47)78-46-40(62)38(60)31(8)69-53(46)72-34/h26-35,38-49,52-57,60-65H,11-25H2,1-10H3/t27?,28?,29?,30?,31-,32-,33+,34+,35-,38-,39-,40+,41+,42-,43-,44-,45+,46-,47-,48-,49-,52+,53+,54+,55+/m1/s1
SMILES CCCCC[C@H]1CCCCCCCCCC(=O)O[C@@H]2[C@H]([C@H](C)O[C@H]([C@@H]2OC(=O)CC(C)C)O[C@@H]2[C@H]([C@@H]([C@@H](COC(=O)C(C)C(C)O)O[C@H]2O[C@@H]2[C@H]([C@@H]([C@@H](C)O[C@H]2O1)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C)O1)OC(=O)C(C)C(C)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1138.61 Volume:   1117.473
?
Van der Waals volume.
Dense:   1.019 LogP:   3.757
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.546
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.35
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   19.0 Rigid Bonds:   46.0
TPSA:   340.88
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   8.0 Rings:   5.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.062 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.887 Fsp3:   0.927
MCE-18:   115.472
?
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:   0.988 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.397 Promiscuous compounds:   0.193

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.665 MDCK Permeability:   -5.021
Pgp-inhibitor:   0.0 Pgp-substrate:   0.682
PAMPA:   0.928
?
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):   0.002
20% Bioavailability (F20%):   0.011 30% Bioavailability (F30%):   0.986
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.158 MRP1:   0.17
Plasma Protein Binding (PPB):   71.314% Volume Distribution (VD):   -0.353
Fu: 18.264%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.558

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.012
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.568
HLM stability:   0.998
?
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):  0.755 Half-life (T1/2):  3.369

ADMET: Toxicity

hERG Blockers:  0.011 hERG Blockers (10um):  0.175
Human Hepatotoxicity (H-HT):  0.669 Drug-induced Liver Injury (DILI):  0.986
AMES Toxicity:  0.872 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.001 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.612 Drug-induced Nephrotoxicity:  0.935
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.608
A549 Cytotoxicity:  0.985 Hek293 Cytotoxicity:  0.194
BCF:   0.383
?
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:   3.261
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.15
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.157
?
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
NPO3955 Ipomoea stans Species Convolvulaceae Eukaryota Roots n.a. n.a. PMID[15387658]
NPO3955 Ipomoea stans Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[8594150]
NPO3955 Ipomoea stans Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT148 Cell line HCT-15 Homo sapiens ED50 > 24.0 ug ml-1 PMID[15387658]
NPT382 Cell line OVCAR-5 Homo sapiens ED50 > 25.0 ug ml-1 PMID[15387658]

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 NPC478731 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
0.9 High Similarity NPC478730
0.878 High Similarity NPC478732
0.8675 High Similarity NPC475270
0.8675 High Similarity NPC475327
0.8659 High Similarity NPC476087
0.8659 High Similarity NPC475667
0.8256 Intermediate Similarity NPC476066
0.814 Intermediate Similarity NPC475525
0.814 Intermediate Similarity NPC475540
0.8068 Intermediate Similarity NPC473605
0.8068 Intermediate Similarity NPC475375
0.7955 Intermediate Similarity NPC475164
0.7471 Intermediate Similarity NPC186992
0.7356 Intermediate Similarity NPC297768
0.7356 Intermediate Similarity NPC173328
0.725 Intermediate Similarity NPC606819
0.7159 Intermediate Similarity NPC479058
0.7045 Intermediate Similarity NPC60849
0.7011 Intermediate Similarity NPC477344
0.6897 Remote Similarity NPC478734
0.6742 Remote Similarity NPC478733
0.6629 Remote Similarity NPC479059
0.6598 Remote Similarity NPC475241
0.6484 Remote Similarity NPC267592
0.6452 Remote Similarity NPC238264
0.6452 Remote Similarity NPC483170
0.6452 Remote Similarity NPC477345
0.6344 Remote Similarity NPC307400
0.6344 Remote Similarity NPC27289
0.6344 Remote Similarity NPC119583
0.6292 Remote Similarity NPC113745
0.6292 Remote Similarity NPC477320
0.6292 Remote Similarity NPC477323
0.6292 Remote Similarity NPC477325
0.6292 Remote Similarity NPC609436
0.6264 Remote Similarity NPC158302
0.625 Remote Similarity NPC281563
0.6211 Remote Similarity NPC115013
0.6196 Remote Similarity NPC109887
0.6186 Remote Similarity NPC269318
0.617 Remote Similarity NPC143421
0.6146 Remote Similarity NPC183888
0.6146 Remote Similarity NPC224953
0.6087 Remote Similarity NPC477326
0.6082 Remote Similarity NPC123204
0.6064 Remote Similarity NPC477319
0.6042 Remote Similarity NPC290012
0.5979 Remote Similarity NPC126685
0.5914 Remote Similarity NPC600446
0.5914 Remote Similarity NPC605013
0.5909 Remote Similarity NPC477350
0.5876 Remote Similarity NPC169345
0.5843 Remote Similarity NPC146380
0.5816 Remote Similarity NPC184915
0.5816 Remote Similarity NPC259294
0.5806 Remote Similarity NPC89843
0.5761 Remote Similarity NPC22742
0.5761 Remote Similarity NPC477346
0.5714 Remote Similarity NPC238056
0.57 Remote Similarity NPC44782
0.5644 Remote Similarity NPC478728
0.5638 Remote Similarity NPC477332
0.5596 Remote Similarity NPC610996
0.5591 Remote Similarity NPC477349
0.5588 Remote Similarity NPC478727
0.5532 Remote Similarity NPC604005
0.5532 Remote Similarity NPC605014
0.5505 Remote Similarity NPC611287
0.5495 Remote Similarity NPC600721
0.5495 Remote Similarity NPC605872
0.5464 Remote Similarity NPC478722
0.5464 Remote Similarity NPC479061
0.5464 Remote Similarity NPC478725
0.5408 Remote Similarity NPC478723
0.5408 Remote Similarity NPC478724
0.5408 Remote Similarity NPC479060
0.54 Remote Similarity NPC477317
0.54 Remote Similarity NPC477318
0.5354 Remote Similarity NPC472204
0.5351 Remote Similarity NPC472352
0.5326 Remote Similarity NPC475425
0.5315 Remote Similarity NPC600672
0.5306 Remote Similarity NPC146992
0.5306 Remote Similarity NPC85759
0.53 Remote Similarity NPC478726
0.5294 Remote Similarity NPC472200
0.5263 Remote Similarity NPC610997
0.5253 Remote Similarity NPC472205
0.52 Remote Similarity NPC294748
0.5196 Remote Similarity NPC479057
0.513 Remote Similarity NPC600940
0.5114 Remote Similarity NPC479056
0.5096 Remote Similarity NPC477347

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478731 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