Natural Product: NPC170666

Natural Product IDNPC170666
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
GAMQIEGJRMEAEJ-BLEIWCCUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968587
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 GAMQIEGJRMEAEJ-BLEIWCCUSA-N
Standard InCHI InChI=1S/C53H86O21/c1-22-32(56)35(59)38(62)44(69-22)74-42-33(57)23(2)70-46(40(42)64)73-41-27(21-68-43-37(61)34(58)26(54)20-67-43)71-45(39(63)36(41)60)72-31-13-14-50(7)28(49(31,5)6)12-15-51(8)29(50)11-10-24-25-18-48(3,4)16-17-53(25,47(65)66)30(55)19-52(24,51)9/h10,22-23,25-46,54-64H,11-21H2,1-9H3,(H,65,66)/t22-,23-,25-,26+,27+,28-,29+,30?,31-,32+,33-,34-,35+,36+,37+,38+,39+,40+,41+,42+,43-,44-,45-,46-,50-,51+,52+,53+/m0/s1
SMILES C[C@H]1[C@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](C)O[C@H]([C@@H]1O)O[C@@H]1[C@@H](CO[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O[C@H]([C@@H]([C@H]1O)O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)CC[C@@]4(C(C[C@@]32C)O)C(=O)O)C1(C)C)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1058.57 Volume:   1027.557
?
Van der Waals volume.
Dense:   1.03 LogP:   1.084
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.827
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.853
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   51.0
TPSA:   333.67
?
Topological Polar Surface Area.
H-Bond Acceptor:   21.0
H-Bond Donor:   12.0 Rings:   9.0
Heavy Atoms:   21.0

MedChem Properties

QED Drug-Likeness Score:   0.103 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.778 Fsp3:   0.943
MCE-18:   197.146
?
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:   0.743 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
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:   0.195 Promiscuous compounds:   0.046

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.175 MDCK Permeability:   -5.113
Pgp-inhibitor:   0.0 Pgp-substrate:   0.255
PAMPA:   1.0
?
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):   0.735
20% Bioavailability (F20%):   0.185 30% Bioavailability (F30%):   0.985
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.011
Plasma Protein Binding (PPB):   58.01% Volume Distribution (VD):   -0.38
Fu: 29.846%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

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:   0.0
CYP3A4-inhibitor:   0.931 CYP3A4-substrate:   0.153
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.635
HLM stability:   0.0
?
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):  -0.344 Half-life (T1/2):  5.027

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.026
Human Hepatotoxicity (H-HT):  0.436 Drug-induced Liver Injury (DILI):  0.703
AMES Toxicity:  0.547 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.004 Skin Sensitization:  0.992
Carcinogencity:  0.01 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.132 Drug-induced Nephrotoxicity:  0.911
Genotoxicity:  0.016 RPMI-8226 Immunitoxicity:  0.118
A549 Cytotoxicity:  0.128 Hek293 Cytotoxicity:  0.174
BCF:   1.268
?
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:   3.877
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.584
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.58
?
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
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. small food enterprises (Zvijezda d.d., Zagreb, Croatia) n.a. DOI[10.1002/EJLT.200900231]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[16660462]
NPO454 Helianthus annuus Species Asteraceae Eukaryota flower petals n.a. n.a. PMID[17480100]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[6361218]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota Tubers n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota Tuber n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Flower Essent. Oil n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17777 Helianthus tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

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

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 NPC170666 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
0.7619 Intermediate Similarity NPC488516
0.7345 Intermediate Similarity NPC475486
0.7157 Intermediate Similarity NPC242611
0.6842 Remote Similarity NPC488515
0.6727 Remote Similarity NPC480424
0.6581 Remote Similarity NPC75318
0.6571 Remote Similarity NPC31839
0.6557 Remote Similarity NPC166422
0.6466 Remote Similarity NPC481082
0.6466 Remote Similarity NPC164419
0.646 Remote Similarity NPC80843
0.6457 Remote Similarity NPC161717
0.6423 Remote Similarity NPC251263
0.6364 Remote Similarity NPC288205
0.6364 Remote Similarity NPC51465
0.632 Remote Similarity NPC54636
0.6303 Remote Similarity NPC324875
0.6303 Remote Similarity NPC292677
0.629 Remote Similarity NPC219180
0.6202 Remote Similarity NPC471385
0.6083 Remote Similarity NPC37134
0.608 Remote Similarity NPC323341
0.6033 Remote Similarity NPC291903
0.5952 Remote Similarity NPC133818
0.5926 Remote Similarity NPC283849
0.5913 Remote Similarity NPC56713
0.5897 Remote Similarity NPC76497
0.5862 Remote Similarity NPC114441
0.5827 Remote Similarity NPC471384
0.582 Remote Similarity NPC276093
0.5812 Remote Similarity NPC6377
0.5812 Remote Similarity NPC208381
0.5794 Remote Similarity NPC473824
0.5785 Remote Similarity NPC257468
0.575 Remote Similarity NPC104400
0.575 Remote Similarity NPC10320
0.575 Remote Similarity NPC180550
0.575 Remote Similarity NPC35405
0.5738 Remote Similarity NPC79718
0.5726 Remote Similarity NPC488209
0.5691 Remote Similarity NPC145899
0.5649 Remote Similarity NPC481080
0.56 Remote Similarity NPC488564
0.5591 Remote Similarity NPC475119
0.5546 Remote Similarity NPC488561
0.5537 Remote Similarity NPC114304
0.5528 Remote Similarity NPC73829
0.5517 Remote Similarity NPC270667
0.5515 Remote Similarity NPC302543
0.5508 Remote Similarity NPC25605
0.5507 Remote Similarity NPC250247
0.5495 Remote Similarity NPC606107
0.5462 Remote Similarity NPC127056
0.5441 Remote Similarity NPC236638
0.5441 Remote Similarity NPC294453
0.5435 Remote Similarity NPC220160
0.5401 Remote Similarity NPC309223
0.5378 Remote Similarity NPC174679
0.5378 Remote Similarity NPC279554
0.5357 Remote Similarity NPC28198
0.5357 Remote Similarity NPC476123
0.5344 Remote Similarity NPC243680
0.5338 Remote Similarity NPC488560
0.5333 Remote Similarity NPC110633
0.5328 Remote Similarity NPC136768
0.5328 Remote Similarity NPC469945
0.5323 Remote Similarity NPC139044
0.5294 Remote Similarity NPC136877
0.5294 Remote Similarity NPC475514
0.5278 Remote Similarity NPC601365
0.5271 Remote Similarity NPC62725
0.5254 Remote Similarity NPC76999
0.5238 Remote Similarity NPC484832
0.5234 Remote Similarity NPC295823
0.5234 Remote Similarity NPC174720
0.5234 Remote Similarity NPC475467
0.5217 Remote Similarity NPC100383
0.5217 Remote Similarity NPC305981
0.5217 Remote Similarity NPC481081
0.5207 Remote Similarity NPC109079
0.52 Remote Similarity NPC258885
0.52 Remote Similarity NPC471383
0.5191 Remote Similarity NPC475287
0.5191 Remote Similarity NPC200788
0.518 Remote Similarity NPC261506
0.518 Remote Similarity NPC4328
0.5156 Remote Similarity NPC323359
0.5147 Remote Similarity NPC476068
0.5145 Remote Similarity NPC43550
0.5141 Remote Similarity NPC102505
0.5141 Remote Similarity NPC488514
0.5126 Remote Similarity NPC164194
0.5122 Remote Similarity NPC22956
0.5109 Remote Similarity NPC13998
0.5077 Remote Similarity NPC481078
0.5075 Remote Similarity NPC123199
0.5072 Remote Similarity NPC41061
0.5072 Remote Similarity NPC227551
0.5041 Remote Similarity NPC12288
0.5038 Remote Similarity NPC123522
0.5038 Remote Similarity NPC11242
0.5038 Remote Similarity NPC280941
0.5038 Remote Similarity NPC235772
0.5037 Remote Similarity NPC475160
0.5037 Remote Similarity NPC475140
0.5037 Remote Similarity NPC473714
0.5036 Remote Similarity NPC21691

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC170666 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