Natural Product: NPC14738

Natural Product IDNPC14738
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
BSPJQLDWNQBHGY-VNHPWOQCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101274440
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal 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 BSPJQLDWNQBHGY-VNHPWOQCSA-N
Standard InCHI InChI=1S/C50H80O23/c1-20-7-12-50(65-18-20)21(2)31-27(73-50)14-49(63)25-6-5-22-13-23(8-10-47(22,3)24(25)9-11-48(31,49)4)66-44-39(62)36(59)40(30(17-53)69-44)70-46-42(72-45-38(61)35(58)33(56)28(15-51)67-45)41(34(57)29(16-52)68-46)71-43-37(60)32(55)26(54)19-64-43/h5,20-21,23-46,51-63H,6-19H2,1-4H3/t20-,21-,23-,24-,25+,26+,27-,28+,29+,30+,31-,32-,33+,34+,35-,36+,37+,38+,39+,40-,41-,42+,43-,44+,45-,46-,47-,48+,49+,50+/m0/s1
SMILES C[C@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@]4([C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)O[C@H]3[C@@H]([C@H]([C@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)O)O)O2)OC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1048.51 Volume:   987.33
?
Van der Waals volume.
Dense:   1.062 LogP:   0.053
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.801
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.535
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   54.0
TPSA:   355.29
?
Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   13.0 Rings:   10.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.09 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.269 Fsp3:   0.96
MCE-18:   264.735
?
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:   0.566 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.275 Promiscuous compounds:   0.042

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.918 MDCK Permeability:   -4.948
Pgp-inhibitor:   0.0 Pgp-substrate:   0.992
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):   0.011
20% Bioavailability (F20%):   0.293 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.005
Plasma Protein Binding (PPB):   48.058% Volume Distribution (VD):   -0.423
Fu: 37.219%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.148
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:   0.09 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.005
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):  -0.351 Half-life (T1/2):  3.713

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.003
Human Hepatotoxicity (H-HT):  0.513 Drug-induced Liver Injury (DILI):  0.927
AMES Toxicity:  0.982 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.06 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.624 Drug-induced Nephrotoxicity:  0.972
Genotoxicity:  0.002 RPMI-8226 Immunitoxicity:  0.347
A549 Cytotoxicity:  0.95 Hek293 Cytotoxicity:  0.813
BCF:   1.057
?
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:   3.263
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.476
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.589
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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
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. root n.a. PMID[16564530]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[29359942]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[31944695]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots; Tubers n.a. n.a. PMID[7714535]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

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 NPC14738 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
0.7049 Intermediate Similarity NPC305771
0.7049 Intermediate Similarity NPC94072
0.7049 Intermediate Similarity NPC169816
0.6923 Remote Similarity NPC31896
0.6838 Remote Similarity NPC477811
0.6803 Remote Similarity NPC15918
0.6532 Remote Similarity NPC210569
0.6522 Remote Similarity NPC97700
0.6522 Remote Similarity NPC30856
0.6348 Remote Similarity NPC300557
0.6311 Remote Similarity NPC167183
0.627 Remote Similarity NPC79900
0.6174 Remote Similarity NPC602423
0.6148 Remote Similarity NPC233433
0.6148 Remote Similarity NPC132080
0.6121 Remote Similarity NPC477809
0.605 Remote Similarity NPC115165
0.6 Remote Similarity NPC263359
0.5984 Remote Similarity NPC473505
0.5969 Remote Similarity NPC32707
0.595 Remote Similarity NPC473518
0.595 Remote Similarity NPC116756
0.595 Remote Similarity NPC309278
0.5938 Remote Similarity NPC477808
0.5902 Remote Similarity NPC232037
0.5877 Remote Similarity NPC470432
0.5877 Remote Similarity NPC230507
0.5862 Remote Similarity NPC475351
0.5859 Remote Similarity NPC477807
0.582 Remote Similarity NPC475333
0.582 Remote Similarity NPC224098
0.582 Remote Similarity NPC208383
0.5814 Remote Similarity NPC220836
0.5806 Remote Similarity NPC476112
0.5806 Remote Similarity NPC307534
0.5798 Remote Similarity NPC6806
0.5758 Remote Similarity NPC244431
0.5667 Remote Similarity NPC249553
0.5659 Remote Similarity NPC480556
0.5636 Remote Similarity NPC181845
0.5625 Remote Similarity NPC470866
0.5581 Remote Similarity NPC94086
0.5581 Remote Similarity NPC473817
0.5574 Remote Similarity NPC184617
0.5547 Remote Similarity NPC232054
0.5546 Remote Similarity NPC473601
0.5528 Remote Similarity NPC475319
0.552 Remote Similarity NPC197003
0.552 Remote Similarity NPC232611
0.5492 Remote Similarity NPC480555
0.5492 Remote Similarity NPC150372
0.5476 Remote Similarity NPC218571
0.5476 Remote Similarity NPC487615
0.536 Remote Similarity NPC475550
0.5312 Remote Similarity NPC83137
0.5304 Remote Similarity NPC250393
0.5285 Remote Similarity NPC51172
0.5285 Remote Similarity NPC49032
0.5271 Remote Similarity NPC480553
0.5259 Remote Similarity NPC206003
0.5259 Remote Similarity NPC473610
0.5246 Remote Similarity NPC470433
0.5246 Remote Similarity NPC46190
0.5246 Remote Similarity NPC171073
0.5238 Remote Similarity NPC269297
0.5238 Remote Similarity NPC222202
0.5234 Remote Similarity NPC470864
0.5227 Remote Similarity NPC190939
0.52 Remote Similarity NPC308459
0.5197 Remote Similarity NPC475625
0.5197 Remote Similarity NPC13193
0.5188 Remote Similarity NPC248202
0.5161 Remote Similarity NPC182900
0.5156 Remote Similarity NPC194207
0.5156 Remote Similarity NPC22779
0.5154 Remote Similarity NPC256983
0.5124 Remote Similarity NPC113044
0.5124 Remote Similarity NPC283829
0.5124 Remote Similarity NPC14704
0.5124 Remote Similarity NPC161676
0.5116 Remote Similarity NPC480554
0.5079 Remote Similarity NPC98018
0.5079 Remote Similarity NPC284104
0.5079 Remote Similarity NPC103616
0.5079 Remote Similarity NPC102016
0.5079 Remote Similarity NPC95051
0.5043 Remote Similarity NPC325828
0.5037 Remote Similarity NPC224314
0.5036 Remote Similarity NPC208832

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC14738 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
0.5043 Remote Similarity NPD8171 Phase 2

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