Natural Product: NPC214458

Natural Product IDNPC214458
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
WOXXEPMRJZSMBS-ZUTGWDQJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968365
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 WOXXEPMRJZSMBS-ZUTGWDQJSA-N
Standard InCHI InChI=1S/C55H88O22/c1-24-34(58)37(61)41(65)46(71-24)76-44-27(20-33(57)69-9)72-45(43(67)39(44)63)70-23-29-36(60)38(62)42(66)48(74-29)77-49(68)55-18-16-50(2,3)21-26(55)25-10-11-31-52(6)14-13-32(75-47-40(64)35(59)28(22-56)73-47)51(4,5)30(52)12-15-54(31,8)53(25,7)17-19-55/h10,24,26-32,34-48,56,58-67H,11-23H2,1-9H3/t24-,26?,27-,28-,29-,30?,31?,32?,34+,35-,36-,37+,38+,39-,40+,41+,42-,43-,44?,45+,46-,47-,48-,52?,53+,54?,55?/m0/s1
SMILES C[C@H]1[C@H]([C@H]([C@H]([C@@H](O1)OC1[C@H](CC(=O)OC)O[C@H]([C@H]([C@@H]1O)O)OC[C@H]1[C@@H]([C@H]([C@@H]([C@@H](O1)OC(=O)C12CCC(C)(C)CC2C2=CCC3C4(C)CCC(C(C)(C)C4CCC3(C)[C@]2(C)CC1)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1100.58 Volume:   1068.303
?
Van der Waals volume.
Dense:   1.03 LogP:   1.882
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.872
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.077
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   51.0
TPSA:   339.74
?
Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   11.0 Rings:   9.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.092 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.76 Fsp3:   0.927
MCE-18:   194.245
?
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:   0.935 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.054
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.16 Promiscuous compounds:   0.007

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.263 MDCK Permeability:   -5.149
Pgp-inhibitor:   0.0 Pgp-substrate:   0.19
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):   0.0
20% Bioavailability (F20%):   0.003 30% Bioavailability (F30%):   0.388
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.774
Plasma Protein Binding (PPB):   69.346% Volume Distribution (VD):   -0.31
Fu: 17.407%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.982
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.0
BSEP inhibitor:   0.92

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:   0.0 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.953
HLM stability:   0.983
?
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):  -0.188 Half-life (T1/2):  4.965

ADMET: Toxicity

hERG Blockers:  0.009 hERG Blockers (10um):  0.261
Human Hepatotoxicity (H-HT):  0.251 Drug-induced Liver Injury (DILI):  0.075
AMES Toxicity:  0.552 Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.015 Skin Sensitization:  0.987
Carcinogencity:  0.001 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.13 Drug-induced Nephrotoxicity:  0.603
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.172
A549 Cytotoxicity:  0.388 Hek293 Cytotoxicity:  0.101
BCF:   1.435
?
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:   4.628
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.409
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.312
?
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
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. leaf n.a. PMID[17125224]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota leaves n.a. n.a. PMID[27400231]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11872 Eleutherococcus senticosus Species Araliaceae 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 NPC214458 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
0.835 Intermediate Similarity NPC295823
0.835 Intermediate Similarity NPC174720
0.835 Intermediate Similarity NPC475467
0.8041 Intermediate Similarity NPC48499
0.787 Intermediate Similarity NPC60557
0.787 Intermediate Similarity NPC67857
0.7818 Intermediate Similarity NPC135904
0.7748 Intermediate Similarity NPC475160
0.7748 Intermediate Similarity NPC473714
0.7679 Intermediate Similarity NPC488560
0.7664 Intermediate Similarity NPC241909
0.7456 Intermediate Similarity NPC481080
0.7451 Intermediate Similarity NPC249848
0.7451 Intermediate Similarity NPC107966
0.7391 Intermediate Similarity NPC476068
0.7358 Intermediate Similarity NPC63159
0.7333 Intermediate Similarity NPC104071
0.7288 Intermediate Similarity NPC305981
0.7265 Intermediate Similarity NPC258617
0.7264 Intermediate Similarity NPC102439
0.7248 Intermediate Similarity NPC481079
0.7232 Intermediate Similarity NPC76972
0.7232 Intermediate Similarity NPC469782
0.7232 Intermediate Similarity NPC204414
0.7227 Intermediate Similarity NPC261506
0.7227 Intermediate Similarity NPC4328
0.7203 Intermediate Similarity NPC43550
0.7196 Intermediate Similarity NPC148417
0.7184 Intermediate Similarity NPC235405
0.717 Intermediate Similarity NPC30735
0.7168 Intermediate Similarity NPC192600
0.7143 Intermediate Similarity NPC236638
0.7143 Intermediate Similarity NPC294453
0.7119 Intermediate Similarity NPC41061
0.7119 Intermediate Similarity NPC227551
0.7075 Intermediate Similarity NPC112352
0.7049 Intermediate Similarity NPC250247
0.7048 Intermediate Similarity NPC295371
0.7037 Intermediate Similarity NPC235438
0.7018 Intermediate Similarity NPC79643
0.6983 Remote Similarity NPC100639
0.6961 Remote Similarity NPC214484
0.6944 Remote Similarity NPC46665
0.6897 Remote Similarity NPC155410
0.686 Remote Similarity NPC481081
0.681 Remote Similarity NPC165204
0.6792 Remote Similarity NPC473373
0.6752 Remote Similarity NPC123199
0.6731 Remote Similarity NPC29069
0.6695 Remote Similarity NPC470218
0.6667 Remote Similarity NPC298034
0.6667 Remote Similarity NPC71065
0.6639 Remote Similarity NPC65105
0.6606 Remote Similarity NPC223301
0.6606 Remote Similarity NPC171544
0.6585 Remote Similarity NPC202828
0.6585 Remote Similarity NPC119592
0.6574 Remote Similarity NPC39211
0.656 Remote Similarity NPC224381
0.6542 Remote Similarity NPC475516
0.6518 Remote Similarity NPC297263
0.6514 Remote Similarity NPC469946
0.6486 Remote Similarity NPC10607
0.6404 Remote Similarity NPC281148
0.6404 Remote Similarity NPC114484
0.6393 Remote Similarity NPC57484
0.6356 Remote Similarity NPC475287
0.6349 Remote Similarity NPC70809
0.6339 Remote Similarity NPC40775
0.6321 Remote Similarity NPC90856
0.629 Remote Similarity NPC475514
0.6283 Remote Similarity NPC475591
0.6283 Remote Similarity NPC236870
0.6261 Remote Similarity NPC104372
0.624 Remote Similarity NPC293330
0.6239 Remote Similarity NPC481078
0.6239 Remote Similarity NPC187290
0.6228 Remote Similarity NPC222580
0.6216 Remote Similarity NPC76497
0.621 Remote Similarity NPC110633
0.6195 Remote Similarity NPC251768
0.6172 Remote Similarity NPC220160
0.6154 Remote Similarity NPC80986
0.6126 Remote Similarity NPC157868
0.6107 Remote Similarity NPC480422
0.6102 Remote Similarity NPC31838
0.6071 Remote Similarity NPC473343
0.6068 Remote Similarity NPC301449
0.6068 Remote Similarity NPC601290
0.6063 Remote Similarity NPC136768
0.6053 Remote Similarity NPC159309
0.6053 Remote Similarity NPC101744
0.6053 Remote Similarity NPC473459
0.6053 Remote Similarity NPC86222
0.6038 Remote Similarity NPC128925
0.6018 Remote Similarity NPC192791
0.5972 Remote Similarity NPC469776
0.5959 Remote Similarity NPC32723
0.5929 Remote Similarity NPC161674
0.5918 Remote Similarity NPC481323
0.5918 Remote Similarity NPC469778
0.5913 Remote Similarity NPC173859
0.5913 Remote Similarity NPC148603
0.5865 Remote Similarity NPC237503
0.5839 Remote Similarity NPC135334
0.5826 Remote Similarity NPC109588
0.5826 Remote Similarity NPC160415
0.5826 Remote Similarity NPC309714
0.5825 Remote Similarity NPC167383
0.5818 Remote Similarity NPC78046
0.58 Remote Similarity NPC481324
0.5776 Remote Similarity NPC164389
0.5776 Remote Similarity NPC488526
0.5776 Remote Similarity NPC480475
0.5769 Remote Similarity NPC309223
0.5763 Remote Similarity NPC134835
0.5752 Remote Similarity NPC173583
0.5727 Remote Similarity NPC204458
0.5726 Remote Similarity NPC68175
0.5702 Remote Similarity NPC473826
0.5678 Remote Similarity NPC475504
0.5676 Remote Similarity NPC1046
0.5649 Remote Similarity NPC295941
0.5645 Remote Similarity NPC123522
0.5597 Remote Similarity NPC102505
0.5597 Remote Similarity NPC480417
0.5597 Remote Similarity NPC488514
0.5583 Remote Similarity NPC73318
0.5581 Remote Similarity NPC286457
0.5574 Remote Similarity NPC104137
0.5574 Remote Similarity NPC26626
0.5565 Remote Similarity NPC473884
0.5565 Remote Similarity NPC470512
0.5556 Remote Similarity NPC480419
0.5545 Remote Similarity NPC209894
0.5541 Remote Similarity NPC469775
0.5533 Remote Similarity NPC469774
0.5524 Remote Similarity NPC45606
0.5517 Remote Similarity NPC263756
0.5517 Remote Similarity NPC213674
0.5512 Remote Similarity NPC471550
0.5493 Remote Similarity NPC472268
0.5492 Remote Similarity NPC96641
0.5492 Remote Similarity NPC163183
0.5478 Remote Similarity NPC150400
0.547 Remote Similarity NPC242840
0.5462 Remote Similarity NPC480418
0.5462 Remote Similarity NPC13998
0.5455 Remote Similarity NPC256798
0.5433 Remote Similarity NPC475209
0.5425 Remote Similarity NPC100925
0.5423 Remote Similarity NPC297950
0.542 Remote Similarity NPC470876
0.5417 Remote Similarity NPC609763
0.5391 Remote Similarity NPC139894
0.5372 Remote Similarity NPC469821
0.5372 Remote Similarity NPC601659
0.5366 Remote Similarity NPC480473
0.5366 Remote Similarity NPC480474
0.536 Remote Similarity NPC114287
0.5355 Remote Similarity NPC469777
0.5354 Remote Similarity NPC470911
0.5345 Remote Similarity NPC58448
0.5333 Remote Similarity NPC470515
0.5323 Remote Similarity NPC36831
0.5299 Remote Similarity NPC302543
0.528 Remote Similarity NPC470915
0.5267 Remote Similarity NPC21691
0.5263 Remote Similarity NPC161717
0.5254 Remote Similarity NPC471547
0.5253 Remote Similarity NPC469772
0.525 Remote Similarity NPC473401
0.5248 Remote Similarity NPC475368
0.5234 Remote Similarity NPC475899
0.5214 Remote Similarity NPC480420
0.5207 Remote Similarity NPC105800
0.5197 Remote Similarity NPC268184
0.5191 Remote Similarity NPC85154
0.5188 Remote Similarity NPC469773
0.5175 Remote Similarity NPC189884
0.5175 Remote Similarity NPC138334
0.517 Remote Similarity NPC220838
0.5167 Remote Similarity NPC471548
0.5164 Remote Similarity NPC470513
0.5154 Remote Similarity NPC191827
0.5132 Remote Similarity NPC472269
0.5122 Remote Similarity NPC64715
0.5113 Remote Similarity NPC473452
0.5091 Remote Similarity NPC306746
0.5091 Remote Similarity NPC199457
0.5086 Remote Similarity NPC475208
0.5083 Remote Similarity NPC75417
0.5077 Remote Similarity NPC309907
0.5071 Remote Similarity NPC8524
0.5051 Remote Similarity NPC162107
0.5051 Remote Similarity NPC46912
0.5045 Remote Similarity NPC68419
0.5043 Remote Similarity NPC250089
0.5043 Remote Similarity NPC136877
0.5043 Remote Similarity NPC157530

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC214458 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