Natural Product: NPC142108

Natural Product IDNPC142108
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
GEWUPLAVRRONRN-LNGDZFGPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
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 GEWUPLAVRRONRN-LNGDZFGPSA-N
Standard InCHI InChI=1S/C63H104O33/c1-22(20-84-55-46(77)43(74)38(69)31(16-64)88-55)8-13-63(83)23(2)36-30(96-63)15-29-27-7-6-25-14-26(9-11-61(25,4)28(27)10-12-62(29,36)5)87-60-54(95-57-48(79)42(73)37(68)24(3)86-57)50(81)52(34(19-67)91-60)93-59-51(82)53(41(72)33(18-66)90-59)94-58-49(80)45(76)40(71)35(92-58)21-85-56-47(78)44(75)39(70)32(17-65)89-56/h6,22-24,26-60,64-83H,7-21H2,1-5H3/t22-,23+,24+,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+,51-,52-,53+,54-,55-,56+,57+,58+,59+,60-,61+,62+,63-/m1/s1
SMILES C[C@H](CC[C@@]1([C@@H](C)[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO[C@@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O2)O)O)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)O)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1388.65 Volume:   1291.524
?
Van der Waals volume.
Dense:   1.075 LogP:   -0.667
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.171
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.289
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   21.0 Rigid Bonds:   60.0
TPSA:   524.59
?
Topological Polar Surface Area.
H-Bond Acceptor:   33.0
H-Bond Donor:   20.0 Rings:   11.0
Heavy Atoms:   33.0

MedChem Properties

QED Drug-Likeness Score:   0.047 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.78 Fsp3:   0.968
MCE-18:   223.403
?
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:   0.477 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
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.446 Promiscuous compounds:   0.043

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.592 MDCK Permeability:   -4.93
Pgp-inhibitor:   0.0 Pgp-substrate:   0.998
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):   0.295
20% Bioavailability (F20%):   0.003 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   24.866% Volume Distribution (VD):   -0.384
Fu: 46.018%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.007
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:   0.017 CYP3A4-substrate:   0.002
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.218
HLM stability:   0.082
?
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):  -1.805 Half-life (T1/2):  5.605

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.495 Drug-induced Liver Injury (DILI):  0.947
AMES Toxicity:  0.985 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 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:  0.404 Drug-induced Nephrotoxicity:  0.991
Genotoxicity:  0.003 RPMI-8226 Immunitoxicity:  0.395
A549 Cytotoxicity:  0.95 Hek293 Cytotoxicity:  0.687
BCF:   1.015
?
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:   3.259
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.478
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.513
?
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
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11599360]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. seed n.a. PMID[21381697]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[37120447]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7639 Senecio isatideus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14100 Persea kusanoi Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2263 Croton megistocarpus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8075 Cacospongia scalaris Species Thorectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7639 Senecio isatideus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8075 Cacospongia scalaris Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2263 Croton megistocarpus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14100 Persea kusanoi Species Lauraceae 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 NPC142108 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
0.875 High Similarity NPC73243
0.875 High Similarity NPC244086
0.875 High Similarity NPC84956
0.8585 High Similarity NPC247037
0.8349 Intermediate Similarity NPC249265
0.8273 Intermediate Similarity NPC23808
0.8273 Intermediate Similarity NPC87998
0.7757 Intermediate Similarity NPC98696
0.7568 Intermediate Similarity NPC102016
0.7568 Intermediate Similarity NPC95051
0.7265 Intermediate Similarity NPC480553
0.7241 Intermediate Similarity NPC218571
0.7241 Intermediate Similarity NPC487615
0.7094 Intermediate Similarity NPC480554
0.7018 Intermediate Similarity NPC475182
0.7009 Intermediate Similarity NPC194207
0.7009 Intermediate Similarity NPC22779
0.6967 Remote Similarity NPC480556
0.6721 Remote Similarity NPC232054
0.6695 Remote Similarity NPC486386
0.6583 Remote Similarity NPC254255
0.6581 Remote Similarity NPC480555
0.6581 Remote Similarity NPC150372
0.6504 Remote Similarity NPC308140
0.646 Remote Similarity NPC94272
0.6371 Remote Similarity NPC287885
0.6325 Remote Similarity NPC470433
0.6325 Remote Similarity NPC46190
0.6325 Remote Similarity NPC171073
0.623 Remote Similarity NPC475333
0.623 Remote Similarity NPC224098
0.623 Remote Similarity NPC208383
0.6148 Remote Similarity NPC470863
0.6134 Remote Similarity NPC122819
0.6124 Remote Similarity NPC224314
0.6016 Remote Similarity NPC269297
0.6016 Remote Similarity NPC222202
0.6 Remote Similarity NPC248746
0.5968 Remote Similarity NPC309278
0.595 Remote Similarity NPC42171
0.5948 Remote Similarity NPC485601
0.5932 Remote Similarity NPC14704
0.5913 Remote Similarity NPC476538
0.5913 Remote Similarity NPC476539
0.5906 Remote Similarity NPC84111
0.5906 Remote Similarity NPC287483
0.5906 Remote Similarity NPC470865
0.5841 Remote Similarity NPC291203
0.5841 Remote Similarity NPC217205
0.5714 Remote Similarity NPC470861
0.5714 Remote Similarity NPC13193
0.5667 Remote Similarity NPC113044
0.5667 Remote Similarity NPC283829
0.5667 Remote Similarity NPC161676
0.5614 Remote Similarity NPC485602
0.5575 Remote Similarity NPC165439
0.5574 Remote Similarity NPC486388
0.5565 Remote Similarity NPC300557
0.5565 Remote Similarity NPC6806
0.55 Remote Similarity NPC306991
0.5481 Remote Similarity NPC477808
0.544 Remote Similarity NPC124677
0.541 Remote Similarity NPC305423
0.5403 Remote Similarity NPC602423
0.5397 Remote Similarity NPC150057
0.5397 Remote Similarity NPC147753
0.536 Remote Similarity NPC477809
0.5354 Remote Similarity NPC98018
0.5354 Remote Similarity NPC284104
0.5354 Remote Similarity NPC103616
0.5285 Remote Similarity NPC485599
0.528 Remote Similarity NPC265275
0.5263 Remote Similarity NPC485600
0.5255 Remote Similarity NPC273002
0.5246 Remote Similarity NPC470432
0.5246 Remote Similarity NPC230507
0.5231 Remote Similarity NPC32361
0.5221 Remote Similarity NPC248202
0.5214 Remote Similarity NPC263359
0.5167 Remote Similarity NPC476540
0.5167 Remote Similarity NPC476541
0.5164 Remote Similarity NPC295980
0.5122 Remote Similarity NPC15249
0.5122 Remote Similarity NPC25455
0.5122 Remote Similarity NPC6295
0.5079 Remote Similarity NPC42482
0.5071 Remote Similarity NPC208832
0.504 Remote Similarity NPC470748

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC142108 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
0.6134 Remote Similarity NPD8449 Approved
0.5397 Remote Similarity NPD8450 Suspended

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